From owner-chemistry@ccl.net Mon Dec 13 01:49:00 2010 From: "Eli Lam elizabeth.shlam-,-gmail.com" To: CCL Subject: CCL: Queries on DFT functional Message-Id: <-43355-101212032453-7211-F7JWvtaVvBygSrJ0Tcblwg(_)server.ccl.net> X-Original-From: "Eli Lam" Date: Sun, 12 Dec 2010 03:24:52 -0500 Sent to CCL by: "Eli Lam" [elizabeth.shlam^-^gmail.com] Hi! I'm quite new to computational chem and have some queries on DFT functional implementation. I've learnt that DFT may underestimate the electron-donating ability of some functional groups and adding more percentage of HF may shift the entire absorption spectrum back to the correct wavelength. So is it HF, which has neglect the electron correlation, will always shift the spectrum to the shorter wavelength? I would like to ask why is neglecting electron correlation can shift the absorption spectrum? Thank you very much! Eli From owner-chemistry@ccl.net Mon Dec 13 02:39:00 2010 From: "Vijay Kumar Tak takvijay*|*gmail.com" To: CCL Subject: CCL:G: Problem in Guassian freq calculation Message-Id: <-43356-101213023410-19586-3w/gm8/3dQVg8DExYkmDgA/a\server.ccl.net> X-Original-From: "Vijay Kumar Tak" Date: Mon, 13 Dec 2010 02:34:09 -0500 Sent to CCL by: "Vijay Kumar Tak" [takvijay!=!gmail.com] Hello, There is a problem in calculating the frequency of an compund carrying a three positive chages. I have optimized the conformation of trication which consist of 88 atoms at B3LYP level. Then i am trying to calculate the frequency of same conformation at the same level, but the out put file is showing following error. ****************************************** Gaussian 09: IA32W-G09RevA.02 11-Jun-2009 11-Dec-2010 ****************************************** %nprocshared=8 Will use up to 8 processors via shared memory. %mem=1GB %chk=E:\Guassian calculations\Trication\DFT-B3LYP\1Freq.chk --------------------------------------------------------------- # freq=noraman cphf=noread b3lyp/6-311+g(d,p) geom=connectivity --------------------------------------------------------------- 1/10=4,30=1,38=1,57=2/1,3; 2/12=2,17=6,18=5,40=1/2; 3/5=4,6=6,7=111,11=2,16=1,25=1,30=1,71=2,74=-5/1,2,3; 4//1; 5/5=2,38=5,98=1/2; 8/6=4,10=90,11=11/1; 11/6=1,8=1,9=11,15=111,16=1/1,2,10; 10/6=1/2; 6/7=2,8=2,9=2,10=2,18=1,28=1/1; 7/8=1,10=1,25=1/1,2,3,16; 1/10=4,30=1/3; 99//99; ----- 1Freq ----- Symbolic Z-matrix: Charge = 3 Multiplicity = 1 C -14.05514 -0.30777 1.48727 C -14.84798 0.78786 1.83187 C -14.72668 1.98553 1.1309 C -13.80815 2.09126 0.08739 C -13.00564 0.99913 -0.25784 C -13.13873 -0.20414 0.4453 C -12.02369 1.11721 -1.39256 N -10.61123 1.31574 -0.91687 C -10.21931 2.04802 0.18506 C -8.85798 2.0396 0.21013 N -8.43244 1.29947 -0.87866 C -9.51721 0.87568 -1.54268 C -7.02846 1.03252 -1.25739 C -6.31137 0.08478 -0.28811 C -4.85723 -0.17144 -0.71843 C -4.1112 -1.10244 0.25006 C -2.66345 -1.3933 -0.18343 C -1.98338 -2.34883 0.80213 N -0.59636 -2.72048 0.42241 C 0.49117 -2.54755 1.18283 N 1.54931 -3.0916 0.57002 C 1.11896 -3.63833 -0.62513 C -0.21873 -3.40475 -0.71828 C 2.90508 -3.24005 1.16662 C 4.05788 -2.79091 0.26352 C 4.15705 -1.27597 0.03719 C 5.32799 -0.84492 -0.86707 C 6.72808 -1.03907 -0.25782 C 7.81353 -0.50618 -1.20285 N 9.18436 -0.67399 -0.67628 C 9.99921 0.31757 -0.28677 N 11.16496 -0.20587 0.09609 C 11.09966 -1.57792 -0.05343 C 9.86287 -1.87229 -0.53766 C 12.36011 0.5472 0.60983 C 12.2046 2.03928 0.49535 C 11.72322 2.78352 1.5785 C 11.59043 4.167 1.47547 C 11.93896 4.81416 0.29083 C 12.42509 4.07915 -0.79052 C 12.55974 2.69678 -0.68887 H -14.16351 -1.24468 2.02048 H -15.56841 0.70225 2.63662 H -15.35334 2.83171 1.38566 H -13.73327 3.01981 -0.46991 H -12.54067 -1.06719 0.16897 H -12.00763 0.21677 -2.00834 H -12.26274 1.9685 -2.0319 H -10.93532 2.49789 0.85127 H -8.17029 2.4977 0.90001 H -9.50739 0.28436 -2.44346 H -7.04881 0.61717 -2.26637 H -6.52158 1.99845 -1.3126 H -6.32711 0.51258 0.71968 H -6.8596 -0.86175 -0.23853 H -4.8469 -0.60934 -1.72349 H -4.32286 0.78307 -0.79029 H -4.10859 -0.65585 1.2512 H -4.65934 -2.04799 0.33501 H -2.66532 -1.83432 -1.18567 H -2.091 -0.46202 -0.2448 H -1.92252 -1.90434 1.79676 H -2.54458 -3.28181 0.8931 H 0.50778 -2.06831 2.14791 H 1.78181 -4.15552 -1.29704 H -0.92084 -3.67961 -1.48655 H 2.89481 -2.66901 2.09656 H 3.01414 -4.29509 1.42588 H 4.96385 -3.16166 0.75273 H 4.00588 -3.31629 -0.69665 H 4.23916 -0.76778 1.00571 H 3.23041 -0.9144 -0.42205 H 5.19336 0.21456 -1.10873 H 5.26553 -1.38324 -1.82042 H 6.91735 -2.09782 -0.05506 H 6.79544 -0.51358 0.70079 H 7.67679 0.56031 -1.38848 H 7.77557 -1.01238 -2.17006 H 9.76587 1.3689 -0.29299 H 11.93069 -2.22061 0.18476 H 9.4258 -2.81868 -0.80634 H 13.21073 0.18858 0.02858 H 12.49515 0.23879 1.64769 H 11.477 2.28761 2.51228 H 11.23562 4.73975 2.32397 H 11.85051 5.89153 0.21621 H 12.71813 4.58395 -1.70328 H 12.96438 2.13382 -1.52421 GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Initialization pass. Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 Number of steps in this run= 2 maximum allowed number of steps= 2. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Stoichiometry C35H47N6(3+) Framework group C1[X(C35H47N6)] Deg. of freedom 258 Full point group C1 NOp 1 Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 -14.055140 -0.307766 1.487270 2 6 0 -14.847981 0.787858 1.831866 3 6 0 -14.726677 1.985534 1.130895 4 6 0 -13.808148 2.091260 0.087392 5 6 0 -13.005645 0.999125 -0.257839 6 6 0 -13.138734 -0.204138 0.445304 7 6 0 -12.023692 1.117210 -1.392560 8 7 0 -10.611225 1.315743 -0.916872 9 6 0 -10.219311 2.048020 0.185057 10 6 0 -8.857979 2.039598 0.210133 11 7 0 -8.432440 1.299473 -0.878655 12 6 0 -9.517207 0.875681 -1.542684 13 6 0 -7.028455 1.032515 -1.257391 14 6 0 -6.311368 0.084778 -0.288110 15 6 0 -4.857232 -0.171438 -0.718427 16 6 0 -4.111197 -1.102435 0.250063 17 6 0 -2.663446 -1.393301 -0.183430 18 6 0 -1.983377 -2.348833 0.802131 19 7 0 -0.596363 -2.720478 0.422409 20 6 0 0.491172 -2.547550 1.182831 21 7 0 1.549314 -3.091600 0.570022 22 6 0 1.118956 -3.638332 -0.625134 23 6 0 -0.218727 -3.404747 -0.718276 24 6 0 2.905076 -3.240050 1.166616 25 6 0 4.057883 -2.790909 0.263519 26 6 0 4.157045 -1.275970 0.037194 27 6 0 5.327988 -0.844917 -0.867068 28 6 0 6.728078 -1.039068 -0.257817 29 6 0 7.813525 -0.506180 -1.202848 30 7 0 9.184359 -0.673991 -0.676284 31 6 0 9.999211 0.317569 -0.286767 32 7 0 11.164957 -0.205873 0.096087 33 6 0 11.099655 -1.577922 -0.053427 34 6 0 9.862871 -1.872290 -0.537662 35 6 0 12.360109 0.547195 0.609832 36 6 0 12.204601 2.039279 0.495350 37 6 0 11.723218 2.783523 1.578500 38 6 0 11.590427 4.166996 1.475465 39 6 0 11.938956 4.814158 0.290826 40 6 0 12.425085 4.079151 -0.790522 41 6 0 12.559738 2.696778 -0.688870 42 1 0 -14.163506 -1.244678 2.020477 43 1 0 -15.568414 0.702249 2.636615 44 1 0 -15.353339 2.831712 1.385663 45 1 0 -13.733274 3.019809 -0.469909 46 1 0 -12.540668 -1.067191 0.168965 47 1 0 -12.007630 0.216772 -2.008343 48 1 0 -12.262742 1.968498 -2.031902 49 1 0 -10.935324 2.497886 0.851274 50 1 0 -8.170292 2.497702 0.900012 51 1 0 -9.507394 0.284364 -2.443457 52 1 0 -7.048810 0.617168 -2.266372 53 1 0 -6.521579 1.998451 -1.312597 54 1 0 -6.327105 0.512579 0.719675 55 1 0 -6.859602 -0.861749 -0.238533 56 1 0 -4.846899 -0.609341 -1.723485 57 1 0 -4.322863 0.783067 -0.790291 58 1 0 -4.108592 -0.655852 1.251203 59 1 0 -4.659344 -2.047986 0.335008 60 1 0 -2.665316 -1.834321 -1.185671 61 1 0 -2.091002 -0.462021 -0.244797 62 1 0 -1.922516 -1.904336 1.796755 63 1 0 -2.544576 -3.281805 0.893097 64 1 0 0.507775 -2.068308 2.147908 65 1 0 1.781806 -4.155525 -1.297041 66 1 0 -0.920844 -3.679609 -1.486549 67 1 0 2.894807 -2.669013 2.096559 68 1 0 3.014140 -4.295093 1.425876 69 1 0 4.963853 -3.161656 0.752730 70 1 0 4.005879 -3.316291 -0.696652 71 1 0 4.239162 -0.767781 1.005710 72 1 0 3.230411 -0.914403 -0.422050 73 1 0 5.193359 0.214561 -1.108726 74 1 0 5.265526 -1.383240 -1.820424 75 1 0 6.917350 -2.097818 -0.055060 76 1 0 6.795441 -0.513577 0.700785 77 1 0 7.676786 0.560314 -1.388484 78 1 0 7.775572 -1.012384 -2.170056 79 1 0 9.765873 1.368902 -0.292993 80 1 0 11.930692 -2.220611 0.184757 81 1 0 9.425801 -2.818683 -0.806338 82 1 0 13.210734 0.188576 0.028579 83 1 0 12.495149 0.238787 1.647686 84 1 0 11.477000 2.287609 2.512282 85 1 0 11.235617 4.739753 2.323972 86 1 0 11.850508 5.891527 0.216208 87 1 0 12.718127 4.583952 -1.703277 88 1 0 12.964379 2.133818 -1.524213 --------------------------------------------------------------------- Rotational constants (GHZ): 0.1679224 0.0103802 0.0099533 Standard basis: 6-311+G(d,p) (5D, 7F) There are 1184 symmetry adapted basis functions of A symmetry. Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 1184 basis functions, 1852 primitive gaussians, 1225 cartesian basis functions 148 alpha electrons 148 beta electrons nuclear repulsion energy 3740.7282424628 Hartrees. NAtoms= 88 NActive= 88 NUniq= 88 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=T Big=T One-electron integrals computed using PRISM. NBasis= 1184 RedAO= T NBF= 1184 NBsUse= 1184 1.00D-06 NBFU= 1184 Harris functional with IExCor= 402 diagonalized for initial guess. ExpMin= 4.38D-02 ExpMax= 6.29D+03 ExpMxC= 9.49D+02 IAcc=2 IRadAn= 0 AccDes= 0.00D+00 HarFok: IExCor= 402 AccDes= 0.00D+00 IRadAn= 0 IDoV= 1 ScaDFX= 1.000000 1.000000 1.000000 1.000000 FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 2001 NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T Omega= 0.000000 0.000000 1.000000 0.000000 0.000000 ICntrl= 500 IOpCl= 0 NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 NMtDT0= 0 I1Cent= 4 NGrid= 0. Petite list used in FoFCou. Initial guess orbital symmetries: Occupied (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) Virtual (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) The electronic state of the initial guess is 1-A. Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. Restarting incremental Fock formation. SCF Done: E(RB3LYP) = -1690.21228532 A.U. after 28 cycles Convg = 0.5107D-08 -V/T = 2.0046 Range of M.O.s used for correlation: 1 1184 NBasis= 1184 NAE= 148 NBE= 148 NFC= 0 NFV= 0 NROrb= 1184 NOA= 148 NOB= 148 NVA= 1036 NVB= 1036 **** Warning!!: The largest alpha MO coefficient is 0.12683417D+03 PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. Symmetrizing basis deriv contribution to polar: IMax=3 JMax=2 DiffMx= 0.00D+00 G2DrvN: will do 4 centers at a time, making 23 passes doing MaxLOS=2. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. FoFDir/FoFCou used for L=0 through L=2. End of G2Drv Frequency-dependent properties file 721 does not exist. End of G2Drv Frequency-dependent properties file 722 does not exist. IDoAtm=11111111111111111111111111111111111111111111111111 IDoAtm=11111111111111111111111111111111111111 Differentiating once with respect to electric field. with respect to dipole field. Differentiating once with respect to nuclear coordinates. There are 267 degrees of freedom in the 1st order CPHF. IDoFFX=5. 267 vectors produced by pass 0 Test12= 1.53D-13 1.00D-09 XBig12= 3.87D+02 6.76D+00. AX will form 15 AO Fock derivatives at one time. 267 vectors produced by pass 1 Test12= 1.53D-13 1.00D-09 XBig12= 8.56D+01 1.11D+00. 264 vectors produced by pass 2 Test12= 1.53D-13 1.00D-09 XBig12= 5.91D-01 5.93D-02. 264 vectors produced by pass 3 Test12= 1.53D-13 1.00D-09 XBig12= 2.23D-03 3.14D-03. 264 vectors produced by pass 4 Test12= 1.53D-13 1.00D-09 XBig12= 4.09D-06 1.29D-04. 264 vectors produced by pass 5 Test12= 1.53D-13 1.00D-09 XBig12= 6.15D-09 4.16D-06. 258 vectors produced by pass 6 Test12= 1.53D-13 1.00D-09 XBig12= 1.40D-11 2.66D-07. 236 vectors produced by pass 7 Test12= 1.53D-13 1.00D-09 XBig12= 5.06D-13 2.87D-08. 219 vectors produced by pass 8 Test12= 1.53D-13 1.00D-09 XBig12= 2.56D-14 6.21D-09. 199 vectors produced by pass 9 Test12= 1.53D-13 1.00D-09 XBig12= 2.12D-14 5.20D-09. 177 vectors produced by pass 10 Test12= 1.53D-13 1.00D-09 XBig12= 2.01D-14 5.01D-09. Internal consistency error detected in FileIO for unit 1 I= 7 J= 0 IFail= 1. dumping /fiocom/, unit = 1 NFiles = 88 SizExt = 32768 WInBlk = 512 defal = F LstWrd = -1962280960 FType=2 FMxFil=10000 Number 0 0 0 0 0 0 0 501 Base 11258363 10315776 73707520 18034688 11021824 362994176-1962321632 23552 End 11720192 10317312 92399104 22244864 11023360 772379936-1962280960 24552 End1 11720192 10317312 92399104 22244864 11023360 772379936-1962280960 24576 Wr Pntr 11258363 10315776 73707520 18034688 11021824 362994176 1757205680 23552 Rd Pntr 11258363 10315776 73707520 18034688 11021824 362994176 1757205680 23552 Length 461829 1536 18691584 4210176 1536 409385760 40672 1000 Number 502 503 507 508 511 514 515 516 Base 275968 96256 97280 284160 225280 5214208 2407936 303104 End 279797 96829 98033 284175 260526 5915728 5214016 2407664 End1 280064 97280 98304 284672 260608 5916160 5214208 2407936 Wr Pntr 275968 96256 97280 284160 225280 5214208 2407936 303104 Rd Pntr 275968 96256 97280 284160 225280 5214208 2407936 303104 Length 3829 573 753 15 35246 701520 2806080 2104560 Number 517 518 520 521 522 523 524 526 Base 10208768 8103936 301568 268800 11019264 10313216 11720192 14526976 End 10312960 10208496 301573 268835 11021632 10315584 13122048 15928832 End1 10313216 10208768 302080 269312 11021824 10315776 13122048 15928832 Wr Pntr 10208768 8103936 301568 268800 11019264 10313216 11720192 14526976 Rd Pntr 10208768 8103936 301568 268800 11019264 10313216 11720192 14526976 Length 104192 2104560 5 35 2368 2368 1401856 1401856 Number 528 530 532 534 536 538 545 547 Base 13122048 10317312 13825024 15928832 16630784 17332736 11025408 11026944 End 13823568 11018832 14526544 16630352 17332304 18034256 11025422 11029312 End1 13824000 11019264 14526976 16630784 17332736 18034688 11025920 11029504 Wr Pntr 13122048 10317312 13825024 15928832 16630784 17332736 11025408 11026944 Rd Pntr 13122048 10317312 13825024 15928832 16630784 17332736 11025408 11026944 Length 701520 701520 701520 701520 701520 701520 14 2368 Number 548 551 552 559 562 563 565 569 Base 22946816 267264 22016 43008 260608 13824000 283648 11024896 End 24348672 267289 22032 43009 266545 13824592 283865 11024897 End1 24348672 267776 22528 43520 266752 13825024 284160 11025408 Wr Pntr 22946816 267264 22016 43008 260608 13824000 283648 11024896 Rd Pntr 22946816 267264 22016 43008 260608 13824000 283648 11024896 Length 1401856 25 16 1 5937 592 217 1 Number 571 575 577 579 580 581 582 583 Base 22244864 100864 282112 266752 41472 282624 280064 43520 End 22946384 225207 282138 266796 42677 283248 281840 43565 End1 22946816 225280 282624 267264 43008 283648 282112 44032 Wr Pntr 22244864 100864 282112 266752 41472 282624 280064 43520 Rd Pntr 22244864 100864 282112 266752 41472 282624 280064 43520 Length 701520 124343 26 44 1205 624 1776 45 Number 584 588 590 598 600 603 605 606 Base 284672 24348672 93810176 44032 11103744 302080 302592 11023360 End 285200 26453232 281116016 44034 11104647 302081 302593 11024544 End1 285696 26453504 281116160 44544 11104768 302592 303104 11024896 Wr Pntr 284672 24348672 93810176 44032 11103744 302080 302592 11023360 Rd Pntr 284672 24348672 93810176 44032 11103744 302080 302592 11023360 Length 528 2104560 187305840 2 903 1 1 1184 Number 607 619 634 670 674 685 694 695 Base 11025920 285696 92399104 269312 98304 5916160 11029504 298496 End 11026512 298421 93809785 275761 98936 7318016 11031872 301252 End1 11026944 298496 93810176 275968 99328 7318016 11032064 301568 Wr Pntr 11025920 285696 92399104 269312 98304 5916160 11029504 298496 Rd Pntr 11025920 285696 92399104 269312 98304 5916160 11029504 298496 Length 592 12725 1410681 6449 632 1401856 2368 2756 Number 698 742 989 991 992 993 994 995 Base 267776 7318016 24576 37888 37376 23040 20480 22528 End 268304 8103928 37076 41169 37381 23140 20510 22538 End1 268800 8103936 37376 41472 37888 23552 20992 23040 Wr Pntr 267776 7318016 24576 37888 37376 23040 20480 22528 Rd Pntr 267776 7318016 24576 37888 37376 23040 20480 22528 Length 528 785912 12500 3281 5 100 30 10 Number 996 997 998 999 2999 3001 3003 3005 Base 21504 99328 20992 44544 11032064 28558848 281116160 69497856 End 21604 100571 21192 95796 11103353 69497424 322054736 71602416 End1 22016 100864 21504 96256 11103744 69497856 322055168 71602688 Wr Pntr 21504 99328 20992 44544 11032064 28558848 281116160 69497856 Rd Pntr 21504 99328 20992 44544 11032064 28558848 281116160 69497856 Length 100 1243 200 51252 71289 40938576 40938576 2104560 Number 3007 3026 9994 9995 9996 9997 9998 9999 Base 71602688 27856896 1181765696 772379936 1757205680 11104768 322055168 26453504 End 73707248 28558416 1757205680 1181765696-1962321632 11258363 362993744 27856544 End1 73707520 28558848 1757205680 1181765696-1962321632 11258363 362994176 27856896 Wr Pntr 71602688 27856896 1181765696 772379936 1757205680 11104768 322055168 26453504 Rd Pntr 71602688 27856896 1181765696 772379936 1757205680 11104768 322055168 26453504 Length 2104560 701520 575439984 409385760 575439984 153595 40938576 1403040 dumping /fiocom/, unit = 2 NFiles = 7 SizExt = 0 WInBlk = 512 defal = F LstWrd = 2838528 FType=2 FMxFil=10000 Number 0 508 522 536 538 634 998 Base 2836784 20480 20695 1433744 2135264 23063 20495 End 2838528 20495 23063 2135264 2836784 1433744 20695 End1 2838528 20495 23063 2135264 2836784 1433744 20695 Wr Pntr 2836784 20480 20695 1433744 2135264 23063 20495 Rd Pntr 2836784 20480 20695 1433744 2135264 23063 20495 Length 1744 15 2368 701520 701520 1410681 200 dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = 512 defal = T LstWrd = 67072 FType=2 FMxFil=10000 Number 0 Base 20480 End 67072 End1 67072 Wr Pntr 20480 Rd Pntr 20480 Length 46592 Error termination in NtrErr: NtrErr called from FIOCnC. Can anybody tell me that what is the problem in my calculation and why it is coming and what is its solution? Thank you very much in advance. With regards, Vijay Tak From owner-chemistry@ccl.net Mon Dec 13 03:53:00 2010 From: "Andrew Voronkov drugdesign*yandex.ru" To: CCL Subject: CCL: software for selective alignment of different elements of the small molecules Message-Id: <-43357-101211153030-21386-hH5AkmdZw1b344wN/CpgZQ%a%server.ccl.net> X-Original-From: Andrew Voronkov Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Sat, 11 Dec 2010 23:30:21 +0300 MIME-Version: 1.0 Sent to CCL by: Andrew Voronkov [drugdesign-x-yandex.ru] Dear CCL users, I'd like to find the software for alignment of the selected small molecule elements. For example I have a series of conformations and I am getting alignment with one shared element, while I'd like to try to use another. Let's say I have parts A, B, C, D and E and I want to get parts D and E alignmed so that I can see the differences in parts A and B orientation. Can you please recommend software packages which can help me to do selective alignment? It would be nice to use something free or with evaluation version. Sincerely yours, Andrey From owner-chemistry@ccl.net Mon Dec 13 04:39:01 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek!=!few.vu.nl" To: CCL Subject: CCL: Queries on DFT functional Message-Id: <-43358-101213043530-22917-uewQPqof42KVb5rOou8ebA[*]server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 13 Dec 2010 10:35:22 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek-,-few.vu.nl] >  I would like to ask why is neglecting electron correlation can shift the absorption > spectrum? This is for almost purely "mathematical" reasons. In HF the orbitals are optimized for the ground state. Any "relaxation" of the orbitals that would happen during excitation is then neglected, because such relaxation comes from doubly and higher excited determinants. The excited state energy is thus computed using non-optimal orbitals, and will therefore be higher than the lowest possible HF energy for the excited state. This is in turn higher than the real excited state energy. However, the neglect of orbital relaxation is the largest error in TDHF. Methods such as CIS(D) or the static exchange approximation (for core excitations) try to fix this error. Sincerely, Ulf Ekstrom From owner-chemistry@ccl.net Mon Dec 13 05:14:00 2010 From: "Eli Lam elizabeth.shlam],[gmail.com" To: CCL Subject: CCL:G: Queries on IOP(3/76=mmmmmnnnnn) in gaussian03 Message-Id: <-43359-101213045739-8061-OEzXQysQi+6tTPYIvgvH5Q]*[server.ccl.net> X-Original-From: "Eli Lam" Date: Mon, 13 Dec 2010 04:57:38 -0500 Sent to CCL by: "Eli Lam" [elizabeth.shlam-*-gmail.com] Hi CCLers, I've got some questions on implementing IOP(3/76=) in gaussian03. It seems that IOP(3/76=mmmmmnnnnn) can adjust the mixing on exchange energy of HF and DFT in calculations. I thought mmmmm+nnnnn has to have a sum of 100%. However, I've found that from http://131.104.156.23/Lectures/CHEM_462/462_Computational.html : "Speaking about B3LYP: B3LYP is obtained from from BLYP, with the following mixing coefficients: BLYP IOp(3/76=1000002000) IOp(3/77=0720008000) IOp(3/78=0810010000)" 1) So, I am confused by why IOP(3/76=mmmmmnnnnn) can have m+n over 100%? 2) I wonder what is the physical meaning of adding more percentage of HF exchange energy? Does it related to the more localization of electron density in the system? 3) For example, I've used PBE1PBE functional for a donor-acceptor (DA) molecule. Isn't PBE1PBE already having 25% HF exchange energy? So if nnnnn=032000, does it mean I have 32% + 25%(originally present in PBE1PBE) HF exchange energy, or indeed I have modified the HF exchange in PBE1PBE to 32% leaving all other functionals untouched? 4) Will the implementation of IOP(3/76) affects the mechanism of the molecule in electronic transition? It seems that the orbitals arrangement differ when I use IOP(3/76) and not using. Just for a little reference, I've calculated a DA molecule with IOP(3/76=10000050000) with the lowest absorption energy at 425.46 nm while using IOP(3/76=10000025000) with that energy at 692.13 nm and that with pure PBE1PBE is at 703 nm. The experimental value for the system is around 550 nm. Thanks a lot! Eli From owner-chemistry@ccl.net Mon Dec 13 05:48:00 2010 From: "Mikko Vainio mikko.vainio__visipoint.fi" To: CCL Subject: CCL: software for selective alignment of different elements of the small molecules Message-Id: <-43360-101213045227-29568-M3wTSdQeb4nERTqA4i74Pg-,-server.ccl.net> X-Original-From: Mikko Vainio Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 13 Dec 2010 11:52:16 +0200 MIME-Version: 1.0 Sent to CCL by: Mikko Vainio [mikko.vainio]=[visipoint.fi] On 12/11/2010 10:30 PM, Andrew Voronkov drugdesign*yandex.ru wrote: > Sent to CCL by: Andrew Voronkov [drugdesign-x-yandex.ru] > > Dear CCL users, > I'd like to find the software for alignment of the selected small molecule elements. For example I have a series of conformations and I am getting alignment with one shared element, while I'd like to try to use another. Let's say I have parts A, B, C, D and E and I want to get parts D and E alignmed so that I can see the differences in parts A and B orientation. Can you please recommend software packages which can help me to do selective alignment? > > It would be nice to use something free or with evaluation version. > > > > Sincerely yours, > Andrey Hi Andrey, This can be achieved using OpenBabel's obfit: http://openbabel.org/wiki/Obfit Cheers, Mikko From owner-chemistry@ccl.net Mon Dec 13 06:24:00 2010 From: "Jens Bredenbeck jbreden _ gmx.de" To: CCL Subject: CCL:G: Relaxed surface scan with frequencies at each point Message-Id: <-43361-101213050823-18327-hzCUM/j4bSjDwyhwPGmofA-*-server.ccl.net> X-Original-From: "Jens Bredenbeck" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Mon, 13 Dec 2010 11:08:15 +0100 MIME-Version: 1.0 Sent to CCL by: "Jens Bredenbeck" [jbreden]=[gmx.de] Dear J. Jules, thanks for the reply. Unfortunatley this choice of keywords (opt=modredundant freq) does not result in a frequency calculation for every point of the surface scan but just in a frequency calculation for the last point of the surface scan. Best regards J. Bredenbeck > The keywords to use are: *opt=modredundant freq. *Obviously, don't forget > to specify coordinates which should be scanned as it would be done in a > rigid scan. For further explanations, read gaussian manual. > > J. Jules. > > On 10 December 2010 22:37, J Bredenbeck jbreden[#]gmx.de < > owner-chemistry^^ccl.net> wrote: > > > > > Sent to CCL by: "J Bredenbeck" [jbreden!=!gmx.de] > > Dear CCL Users, > > > > I would like to do a relaxed surface scan in Gaussian03 with a normal > mode > > calculation at each point after optimization. I would be great if > somebody > > could tell me how this type of calculation can be set up. > > > > Regards, > > Jens> > > > > > > > -- > J. Jules. -- Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail From owner-chemistry@ccl.net Mon Dec 13 06:58:00 2010 From: "Chris Swain swain(0)mac.com" To: CCL Subject: CCL: software for selective alignment of different elements of the small molecules Message-Id: <-43362-101213052024-15110-l1+5zn3nN7gd/fIkuQHvPQ!^!server.ccl.net> X-Original-From: Chris Swain Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Mon, 13 Dec 2010 10:19:47 +0000 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain!A!mac.com] OpenBabel allows overlays based on SMARTS http://openbabel.org/wiki/Obfit On 11 Dec 2010, at 20:30, Andrew Voronkov drugdesign*yandex.ru wrote: > > Sent to CCL by: Andrew Voronkov [drugdesign-x-yandex.ru] > > Dear CCL users, > I'd like to find the software for alignment of the selected small molecule elements. For example I have a series of conformations and I am getting alignment with one shared element, while I'd like to try to use another. Let's say I have parts A, B, C, D and E and I want to get parts D and E alignmed so that I can see the differences in parts A and B orientation. Can you please recommend software packages which can help me to do selective alignment? > > It would be nice to use something free or with evaluation version. > > > > Sincerely yours, > Andrey> > From owner-chemistry@ccl.net Mon Dec 13 07:34:01 2010 From: "Justin Finnerty justin.finnerty~!~uni-oldenburg.de" To: CCL Subject: CCL:G: Problem in Guassian freq calculation Message-Id: <-43363-101213070346-13601-L1U5r0UD2KXMMwXAru7CAQ],[server.ccl.net> X-Original-From: Justin Finnerty Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 13 Dec 2010 13:03:36 +0100 Mime-Version: 1.0 Sent to CCL by: Justin Finnerty [justin.finnerty=-=uni-oldenburg.de] Dear Vijay, > Internal consistency error detected in FileIO for unit 1 I= 7 J= 0 IFail= 1. > > > dumping /fiocom/, unit = 1 NFiles = 88 SizExt = 32768 WInBlk = 512 > defal = F LstWrd = -1962280960 FType=2 FMxFil=10000 Gaussian errors like this indicate missing information in your input or checkpoint file. > --------------------------------------------------------------- > # freq=noraman cphf=noread b3lyp/6-311+g(d,p) geom=connectivity > --------------------------------------------------------------- In this case I am guessing it is because you specify "geom=connectivity" but have not put a connectivity section in your input, you only put the geometry. Now you may say "it has worked before!" and I say "welcome to the wonderful world of gaussian input files!". I say this because the connectivity section of an input file can be *empty* and gaussian will detect this depending on the number of empty lines after the geometry! So simply adding a few blank lines to the end of your input file can be the difference between a failed or successful calculation. From owner-chemistry@ccl.net Mon Dec 13 08:09:01 2010 From: "=?iso-8859-15?q?=D6d=F6n_Farkas?= farkas]*[chem.elte.hu" To: CCL Subject: CCL:G: Problem in Guassian freq calculation Message-Id: <-43364-101213070949-20101-MFxjwMaRh9khpMkFV4usLw~!~server.ccl.net> X-Original-From: =?iso-8859-15?q?=D6d=F6n_Farkas?= Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Mon, 13 Dec 2010 13:09:29 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-15?q?=D6d=F6n_Farkas?= [farkas*chem.elte.hu] Hi Vijay, I'm pretty sure you have ran out of disk space. Anyway, for frequency jobs give as much memory you can. Best wishes, Odon Odon Farkas Associate Professor Laboratory of Chemical Informatics Institute of Chemistry Eötvös Loránd University, Budapest 1/A Pázmány Péter sétány H-1117 Budapest, Hungary Cellphone: +36-30-2553111 On Monday 13 December 2010 08:34:09 Vijay Kumar Tak takvijay*|*gmail.com wrote: > Sent to CCL by: "Vijay Kumar Tak" [takvijay!=!gmail.com] > Hello, > There is a problem in calculating the frequency of an compund carrying a > three positive chages. I have optimized the conformation of trication which > consist of 88 atoms at B3LYP level. Then i am trying to calculate the > frequency of same conformation at the same level, but the out put file is > showing following error. ****************************************** > Gaussian 09: IA32W-G09RevA.02 11-Jun-2009 > 11-Dec-2010 > ****************************************** > %nprocshared=8 > Will use up to 8 processors via shared memory. > %mem=1GB > %chk=E:\Guassian calculations\Trication\DFT-B3LYP\1Freq.chk > --------------------------------------------------------------- > # freq=noraman cphf=noread b3lyp/6-311+g(d,p) geom=connectivity > --------------------------------------------------------------- > 1/10=4,30=1,38=1,57=2/1,3; > 2/12=2,17=6,18=5,40=1/2; > 3/5=4,6=6,7=111,11=2,16=1,25=1,30=1,71=2,74=-5/1,2,3; > 4//1; > 5/5=2,38=5,98=1/2; > 8/6=4,10=90,11=11/1; > 11/6=1,8=1,9=11,15=111,16=1/1,2,10; > 10/6=1/2; > 6/7=2,8=2,9=2,10=2,18=1,28=1/1; > 7/8=1,10=1,25=1/1,2,3,16; > 1/10=4,30=1/3; > 99//99; > ----- > 1Freq > ----- > Symbolic Z-matrix: > Charge = 3 Multiplicity = 1 > C -14.05514 -0.30777 1.48727 > C -14.84798 0.78786 1.83187 > C -14.72668 1.98553 1.1309 > C -13.80815 2.09126 0.08739 > C -13.00564 0.99913 -0.25784 > C -13.13873 -0.20414 0.4453 > C -12.02369 1.11721 -1.39256 > N -10.61123 1.31574 -0.91687 > C -10.21931 2.04802 0.18506 > C -8.85798 2.0396 0.21013 > N -8.43244 1.29947 -0.87866 > C -9.51721 0.87568 -1.54268 > C -7.02846 1.03252 -1.25739 > C -6.31137 0.08478 -0.28811 > C -4.85723 -0.17144 -0.71843 > C -4.1112 -1.10244 0.25006 > C -2.66345 -1.3933 -0.18343 > C -1.98338 -2.34883 0.80213 > N -0.59636 -2.72048 0.42241 > C 0.49117 -2.54755 1.18283 > N 1.54931 -3.0916 0.57002 > C 1.11896 -3.63833 -0.62513 > C -0.21873 -3.40475 -0.71828 > C 2.90508 -3.24005 1.16662 > C 4.05788 -2.79091 0.26352 > C 4.15705 -1.27597 0.03719 > C 5.32799 -0.84492 -0.86707 > C 6.72808 -1.03907 -0.25782 > C 7.81353 -0.50618 -1.20285 > N 9.18436 -0.67399 -0.67628 > C 9.99921 0.31757 -0.28677 > N 11.16496 -0.20587 0.09609 > C 11.09966 -1.57792 -0.05343 > C 9.86287 -1.87229 -0.53766 > C 12.36011 0.5472 0.60983 > C 12.2046 2.03928 0.49535 > C 11.72322 2.78352 1.5785 > C 11.59043 4.167 1.47547 > C 11.93896 4.81416 0.29083 > C 12.42509 4.07915 -0.79052 > C 12.55974 2.69678 -0.68887 > H -14.16351 -1.24468 2.02048 > H -15.56841 0.70225 2.63662 > H -15.35334 2.83171 1.38566 > H -13.73327 3.01981 -0.46991 > H -12.54067 -1.06719 0.16897 > H -12.00763 0.21677 -2.00834 > H -12.26274 1.9685 -2.0319 > H -10.93532 2.49789 0.85127 > H -8.17029 2.4977 0.90001 > H -9.50739 0.28436 -2.44346 > H -7.04881 0.61717 -2.26637 > H -6.52158 1.99845 -1.3126 > H -6.32711 0.51258 0.71968 > H -6.8596 -0.86175 -0.23853 > H -4.8469 -0.60934 -1.72349 > H -4.32286 0.78307 -0.79029 > H -4.10859 -0.65585 1.2512 > H -4.65934 -2.04799 0.33501 > H -2.66532 -1.83432 -1.18567 > H -2.091 -0.46202 -0.2448 > H -1.92252 -1.90434 1.79676 > H -2.54458 -3.28181 0.8931 > H 0.50778 -2.06831 2.14791 > H 1.78181 -4.15552 -1.29704 > H -0.92084 -3.67961 -1.48655 > H 2.89481 -2.66901 2.09656 > H 3.01414 -4.29509 1.42588 > H 4.96385 -3.16166 0.75273 > H 4.00588 -3.31629 -0.69665 > H 4.23916 -0.76778 1.00571 > H 3.23041 -0.9144 -0.42205 > H 5.19336 0.21456 -1.10873 > H 5.26553 -1.38324 -1.82042 > H 6.91735 -2.09782 -0.05506 > H 6.79544 -0.51358 0.70079 > H 7.67679 0.56031 -1.38848 > H 7.77557 -1.01238 -2.17006 > H 9.76587 1.3689 -0.29299 > H 11.93069 -2.22061 0.18476 > H 9.4258 -2.81868 -0.80634 > H 13.21073 0.18858 0.02858 > H 12.49515 0.23879 1.64769 > H 11.477 2.28761 2.51228 > H 11.23562 4.73975 2.32397 > H 11.85051 5.89153 0.21621 > H 12.71813 4.58395 -1.70328 > H 12.96438 2.13382 -1.52421 > > > GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad > Berny optimization. > Initialization pass. > Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 > Number of steps in this run= 2 maximum allowed number of steps= 2. > GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad > > Stoichiometry C35H47N6(3+) > Framework group C1[X(C35H47N6)] > Deg. of freedom 258 > Full point group C1 NOp 1 > Largest Abelian subgroup C1 NOp 1 > Largest concise Abelian subgroup C1 NOp 1 > Standard orientation: > --------------------------------------------------------------------- > Center Atomic Atomic Coordinates (Angstroms) > Number Number Type X Y Z > --------------------------------------------------------------------- > 1 6 0 -14.055140 -0.307766 1.487270 > 2 6 0 -14.847981 0.787858 1.831866 > 3 6 0 -14.726677 1.985534 1.130895 > 4 6 0 -13.808148 2.091260 0.087392 > 5 6 0 -13.005645 0.999125 -0.257839 > 6 6 0 -13.138734 -0.204138 0.445304 > 7 6 0 -12.023692 1.117210 -1.392560 > 8 7 0 -10.611225 1.315743 -0.916872 > 9 6 0 -10.219311 2.048020 0.185057 > 10 6 0 -8.857979 2.039598 0.210133 > 11 7 0 -8.432440 1.299473 -0.878655 > 12 6 0 -9.517207 0.875681 -1.542684 > 13 6 0 -7.028455 1.032515 -1.257391 > 14 6 0 -6.311368 0.084778 -0.288110 > 15 6 0 -4.857232 -0.171438 -0.718427 > 16 6 0 -4.111197 -1.102435 0.250063 > 17 6 0 -2.663446 -1.393301 -0.183430 > 18 6 0 -1.983377 -2.348833 0.802131 > 19 7 0 -0.596363 -2.720478 0.422409 > 20 6 0 0.491172 -2.547550 1.182831 > 21 7 0 1.549314 -3.091600 0.570022 > 22 6 0 1.118956 -3.638332 -0.625134 > 23 6 0 -0.218727 -3.404747 -0.718276 > 24 6 0 2.905076 -3.240050 1.166616 > 25 6 0 4.057883 -2.790909 0.263519 > 26 6 0 4.157045 -1.275970 0.037194 > 27 6 0 5.327988 -0.844917 -0.867068 > 28 6 0 6.728078 -1.039068 -0.257817 > 29 6 0 7.813525 -0.506180 -1.202848 > 30 7 0 9.184359 -0.673991 -0.676284 > 31 6 0 9.999211 0.317569 -0.286767 > 32 7 0 11.164957 -0.205873 0.096087 > 33 6 0 11.099655 -1.577922 -0.053427 > 34 6 0 9.862871 -1.872290 -0.537662 > 35 6 0 12.360109 0.547195 0.609832 > 36 6 0 12.204601 2.039279 0.495350 > 37 6 0 11.723218 2.783523 1.578500 > 38 6 0 11.590427 4.166996 1.475465 > 39 6 0 11.938956 4.814158 0.290826 > 40 6 0 12.425085 4.079151 -0.790522 > 41 6 0 12.559738 2.696778 -0.688870 > 42 1 0 -14.163506 -1.244678 2.020477 > 43 1 0 -15.568414 0.702249 2.636615 > 44 1 0 -15.353339 2.831712 1.385663 > 45 1 0 -13.733274 3.019809 -0.469909 > 46 1 0 -12.540668 -1.067191 0.168965 > 47 1 0 -12.007630 0.216772 -2.008343 > 48 1 0 -12.262742 1.968498 -2.031902 > 49 1 0 -10.935324 2.497886 0.851274 > 50 1 0 -8.170292 2.497702 0.900012 > 51 1 0 -9.507394 0.284364 -2.443457 > 52 1 0 -7.048810 0.617168 -2.266372 > 53 1 0 -6.521579 1.998451 -1.312597 > 54 1 0 -6.327105 0.512579 0.719675 > 55 1 0 -6.859602 -0.861749 -0.238533 > 56 1 0 -4.846899 -0.609341 -1.723485 > 57 1 0 -4.322863 0.783067 -0.790291 > 58 1 0 -4.108592 -0.655852 1.251203 > 59 1 0 -4.659344 -2.047986 0.335008 > 60 1 0 -2.665316 -1.834321 -1.185671 > 61 1 0 -2.091002 -0.462021 -0.244797 > 62 1 0 -1.922516 -1.904336 1.796755 > 63 1 0 -2.544576 -3.281805 0.893097 > 64 1 0 0.507775 -2.068308 2.147908 > 65 1 0 1.781806 -4.155525 -1.297041 > 66 1 0 -0.920844 -3.679609 -1.486549 > 67 1 0 2.894807 -2.669013 2.096559 > 68 1 0 3.014140 -4.295093 1.425876 > 69 1 0 4.963853 -3.161656 0.752730 > 70 1 0 4.005879 -3.316291 -0.696652 > 71 1 0 4.239162 -0.767781 1.005710 > 72 1 0 3.230411 -0.914403 -0.422050 > 73 1 0 5.193359 0.214561 -1.108726 > 74 1 0 5.265526 -1.383240 -1.820424 > 75 1 0 6.917350 -2.097818 -0.055060 > 76 1 0 6.795441 -0.513577 0.700785 > 77 1 0 7.676786 0.560314 -1.388484 > 78 1 0 7.775572 -1.012384 -2.170056 > 79 1 0 9.765873 1.368902 -0.292993 > 80 1 0 11.930692 -2.220611 0.184757 > 81 1 0 9.425801 -2.818683 -0.806338 > 82 1 0 13.210734 0.188576 0.028579 > 83 1 0 12.495149 0.238787 1.647686 > 84 1 0 11.477000 2.287609 2.512282 > 85 1 0 11.235617 4.739753 2.323972 > 86 1 0 11.850508 5.891527 0.216208 > 87 1 0 12.718127 4.583952 -1.703277 > 88 1 0 12.964379 2.133818 -1.524213 > --------------------------------------------------------------------- > Rotational constants (GHZ): 0.1679224 0.0103802 0.0099533 > Standard basis: 6-311+G(d,p) (5D, 7F) > There are 1184 symmetry adapted basis functions of A symmetry. > Integral buffers will be 262144 words long. > Raffenetti 2 integral format. > Two-electron integral symmetry is turned on. > 1184 basis functions, 1852 primitive gaussians, 1225 cartesian basis > functions 148 alpha electrons 148 beta electrons > nuclear repulsion energy 3740.7282424628 Hartrees. > NAtoms= 88 NActive= 88 NUniq= 88 SFac= 7.50D-01 NAtFMM= 80 > NAOKFM=T Big=T One-electron integrals computed using PRISM. > NBasis= 1184 RedAO= T NBF= 1184 > NBsUse= 1184 1.00D-06 NBFU= 1184 > Harris functional with IExCor= 402 diagonalized for initial guess. > ExpMin= 4.38D-02 ExpMax= 6.29D+03 ExpMxC= 9.49D+02 IAcc=2 IRadAn= > 0 AccDes= 0.00D+00 HarFok: IExCor= 402 AccDes= 0.00D+00 IRadAn= 0 > IDoV= 1 > ScaDFX= 1.000000 1.000000 1.000000 1.000000 > FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 2001 > NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T > Omega= 0.000000 0.000000 1.000000 0.000000 0.000000 ICntrl= > 500 IOpCl= 0 NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= > 0 NMtDT0= 0 I1Cent= 4 NGrid= 0. > Petite list used in FoFCou. > Initial guess orbital symmetries: > Occupied (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) > Virtual (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) > The electronic state of the initial guess is 1-A. > Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. > Requested convergence on MAX density matrix=1.00D-06. > Requested convergence on energy=1.00D-06. > No special actions if energy rises. > Restarting incremental Fock formation. > SCF Done: E(RB3LYP) = -1690.21228532 A.U. after 28 cycles > Convg = 0.5107D-08 -V/T = 2.0046 > Range of M.O.s used for correlation: 1 1184 > NBasis= 1184 NAE= 148 NBE= 148 NFC= 0 NFV= 0 > NROrb= 1184 NOA= 148 NOB= 148 NVA= 1036 NVB= 1036 > > **** Warning!!: The largest alpha MO coefficient is 0.12683417D+03 > > PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. > PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. > Symmetrizing basis deriv contribution to polar: > IMax=3 JMax=2 DiffMx= 0.00D+00 > G2DrvN: will do 4 centers at a time, making 23 passes doing > MaxLOS=2. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling > FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, > ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= > 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 > FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T > I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= > 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= > 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling > FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, > ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= > 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 > FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T > I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= > 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= > 0.00D+00. Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling > FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, > ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. Calling FoFCou, ICntrl= > 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. FoFDir/FoFCou used for L=0 through > L=2. > End of G2Drv Frequency-dependent properties file 721 does not exist. > End of G2Drv Frequency-dependent properties file 722 does not exist. > IDoAtm=11111111111111111111111111111111111111111111111111 > IDoAtm=11111111111111111111111111111111111111 > Differentiating once with respect to electric field. > with respect to dipole field. > Differentiating once with respect to nuclear coordinates. > There are 267 degrees of freedom in the 1st order CPHF. > IDoFFX=5. 267 vectors produced by pass 0 Test12= 1.53D-13 1.00D-09 XBig12= > 3.87D+02 6.76D+00. AX will form 15 AO Fock derivatives at one time. > 267 vectors produced by pass 1 Test12= 1.53D-13 1.00D-09 XBig12= > 8.56D+01 1.11D+00. 264 vectors produced by pass 2 Test12= 1.53D-13 > 1.00D-09 XBig12= 5.91D-01 5.93D-02. 264 vectors produced by pass 3 Test12= > 1.53D-13 1.00D-09 XBig12= 2.23D-03 3.14D-03. 264 vectors produced by pass > 4 Test12= 1.53D-13 1.00D-09 XBig12= 4.09D-06 1.29D-04. 264 vectors produced > by pass 5 Test12= 1.53D-13 1.00D-09 XBig12= 6.15D-09 4.16D-06. 258 vectors > produced by pass 6 Test12= 1.53D-13 1.00D-09 XBig12= 1.40D-11 2.66D-07. > 236 vectors produced by pass 7 Test12= 1.53D-13 1.00D-09 XBig12= 5.06D-13 > 2.87D-08. 219 vectors produced by pass 8 Test12= 1.53D-13 1.00D-09 XBig12= > 2.56D-14 6.21D-09. 199 vectors produced by pass 9 Test12= 1.53D-13 > 1.00D-09 XBig12= 2.12D-14 5.20D-09. 177 vectors produced by pass 10 Test12= > 1.53D-13 1.00D-09 XBig12= 2.01D-14 5.01D-09. Internal consistency error > detected in FileIO for unit 1 I= 7 J= 0 IFail= 1. > > > dumping /fiocom/, unit = 1 NFiles = 88 SizExt = 32768 WInBlk = > 512 defal = F LstWrd = -1962280960 FType=2 FMxFil=10000 > > Number 0 0 0 0 0 0 > 0 501 Base 11258363 10315776 73707520 18034688 > 11021824 362994176-1962321632 23552 End 11720192 10317312 > 92399104 22244864 11023360 772379936-1962280960 24552 End1 > 11720192 10317312 92399104 22244864 11023360 772379936-1962280960 > 24576 Wr Pntr 11258363 10315776 73707520 18034688 11021824 > 362994176 1757205680 23552 Rd Pntr 11258363 10315776 73707520 > 18034688 11021824 362994176 1757205680 23552 Length 461829 > 1536 18691584 4210176 1536 409385760 40672 1000 > > Number 502 503 507 508 511 514 > 515 516 Base 275968 96256 97280 284160 > 225280 5214208 2407936 303104 End 279797 96829 > 98033 284175 260526 5915728 5214016 2407664 End1 > 280064 97280 98304 284672 260608 5916160 5214208 > 2407936 Wr Pntr 275968 96256 97280 284160 225280 > 5214208 2407936 303104 Rd Pntr 275968 96256 97280 > 284160 225280 5214208 2407936 303104 Length 3829 > 573 753 15 35246 701520 2806080 2104560 > > Number 517 518 520 521 522 523 > 524 526 Base 10208768 8103936 301568 268800 > 11019264 10313216 11720192 14526976 End 10312960 10208496 > 301573 268835 11021632 10315584 13122048 15928832 End1 > 10313216 10208768 302080 269312 11021824 10315776 13122048 > 15928832 Wr Pntr 10208768 8103936 301568 268800 11019264 > 10313216 11720192 14526976 Rd Pntr 10208768 8103936 301568 > 268800 11019264 10313216 11720192 14526976 Length 104192 > 2104560 5 35 2368 2368 1401856 1401856 > > Number 528 530 532 534 536 538 > 545 547 Base 13122048 10317312 13825024 15928832 > 16630784 17332736 11025408 11026944 End 13823568 11018832 > 14526544 16630352 17332304 18034256 11025422 11029312 End1 > 13824000 11019264 14526976 16630784 17332736 18034688 11025920 > 11029504 Wr Pntr 13122048 10317312 13825024 15928832 16630784 > 17332736 11025408 11026944 Rd Pntr 13122048 10317312 13825024 > 15928832 16630784 17332736 11025408 11026944 Length 701520 > 701520 701520 701520 701520 701520 14 2368 > > Number 548 551 552 559 562 563 > 565 569 Base 22946816 267264 22016 43008 > 260608 13824000 283648 11024896 End 24348672 267289 > 22032 43009 266545 13824592 283865 11024897 End1 > 24348672 267776 22528 43520 266752 13825024 284160 > 11025408 Wr Pntr 22946816 267264 22016 43008 260608 > 13824000 283648 11024896 Rd Pntr 22946816 267264 22016 > 43008 260608 13824000 283648 11024896 Length 1401856 > 25 16 1 5937 592 217 1 > > Number 571 575 577 579 580 581 > 582 583 Base 22244864 100864 282112 266752 > 41472 282624 280064 43520 End 22946384 225207 > 282138 266796 42677 283248 281840 43565 End1 > 22946816 225280 282624 267264 43008 283648 282112 > 44032 Wr Pntr 22244864 100864 282112 266752 41472 > 282624 280064 43520 Rd Pntr 22244864 100864 282112 > 266752 41472 282624 280064 43520 Length 701520 > 124343 26 44 1205 624 1776 45 > > Number 584 588 590 598 600 603 > 605 606 Base 284672 24348672 93810176 44032 > 11103744 302080 302592 11023360 End 285200 26453232 > 281116016 44034 11104647 302081 302593 11024544 End1 > 285696 26453504 281116160 44544 11104768 302592 303104 > 11024896 Wr Pntr 284672 24348672 93810176 44032 11103744 > 302080 302592 11023360 Rd Pntr 284672 24348672 93810176 > 44032 11103744 302080 302592 11023360 Length 528 > 2104560 187305840 2 903 1 1 1184 > > Number 607 619 634 670 674 685 > 694 695 Base 11025920 285696 92399104 269312 > 98304 5916160 11029504 298496 End 11026512 298421 > 93809785 275761 98936 7318016 11031872 301252 End1 > 11026944 298496 93810176 275968 99328 7318016 11032064 > 301568 Wr Pntr 11025920 285696 92399104 269312 98304 > 5916160 11029504 298496 Rd Pntr 11025920 285696 92399104 > 269312 98304 5916160 11029504 298496 Length 592 > 12725 1410681 6449 632 1401856 2368 2756 > > Number 698 742 989 991 992 993 > 994 995 Base 267776 7318016 24576 37888 > 37376 23040 20480 22528 End 268304 8103928 > 37076 41169 37381 23140 20510 22538 End1 > 268800 8103936 37376 41472 37888 23552 20992 > 23040 Wr Pntr 267776 7318016 24576 37888 37376 > 23040 20480 22528 Rd Pntr 267776 7318016 24576 > 37888 37376 23040 20480 22528 Length 528 > 785912 12500 3281 5 100 30 10 > > Number 996 997 998 999 2999 3001 > 3003 3005 Base 21504 99328 20992 44544 > 11032064 28558848 281116160 69497856 End 21604 100571 > 21192 95796 11103353 69497424 322054736 71602416 End1 > 22016 100864 21504 96256 11103744 69497856 322055168 > 71602688 Wr Pntr 21504 99328 20992 44544 11032064 > 28558848 281116160 69497856 Rd Pntr 21504 99328 20992 > 44544 11032064 28558848 281116160 69497856 Length 100 > 1243 200 51252 71289 40938576 40938576 2104560 > > Number 3007 3026 9994 9995 9996 9997 > 9998 9999 Base 71602688 27856896 1181765696 772379936 > 1757205680 11104768 322055168 26453504 End 73707248 28558416 > 1757205680 1181765696-1962321632 11258363 362993744 27856544 End1 > 73707520 28558848 1757205680 1181765696-1962321632 11258363 362994176 > 27856896 Wr Pntr 71602688 27856896 1181765696 772379936 1757205680 > 11104768 322055168 26453504 Rd Pntr 71602688 27856896 1181765696 > 772379936 1757205680 11104768 322055168 26453504 Length 2104560 > 701520 575439984 409385760 575439984 153595 40938576 1403040 > > > dumping /fiocom/, unit = 2 NFiles = 7 SizExt = 0 WInBlk = > 512 defal = F LstWrd = 2838528 FType=2 FMxFil=10000 > > Number 0 508 522 536 538 634 > 998 Base 2836784 20480 20695 1433744 2135264 > 23063 20495 End 2838528 20495 23063 2135264 > 2836784 1433744 20695 End1 2838528 20495 23063 > 2135264 2836784 1433744 20695 Wr Pntr 2836784 20480 > 20695 1433744 2135264 23063 20495 Rd Pntr 2836784 > 20480 20695 1433744 2135264 23063 20495 Length > 1744 15 2368 701520 701520 1410681 200 > > > dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = > 512 defal = T LstWrd = 67072 FType=2 FMxFil=10000 > > Number 0 > Base 20480 > End 67072 > End1 67072 > Wr Pntr 20480 > Rd Pntr 20480 > Length 46592 > Error termination in NtrErr: > NtrErr called from FIOCnC. > > Can anybody tell me that what is the problem in my calculation and why it > is coming and what is its solution? Thank you very much in advance. With > regards, > Vijay Tak From owner-chemistry@ccl.net Mon Dec 13 08:44:00 2010 From: "P.D.Jarowski##surrey.ac.uk" To: CCL Subject: CCL: Schematic optimization sequence Message-Id: <-43365-101213072850-14557-luM187MdJinC4imBWAUZWA^_^server.ccl.net> X-Original-From: Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_7573C7C772F1CB48A79EA49CDD41DD3DE90EE41EC9EXMB01CMSsurr_" Date: Mon, 13 Dec 2010 12:28:37 +0000 MIME-Version: 1.0 Sent to CCL by: [P.D.Jarowski|-|surrey.ac.uk] --_000_7573C7C772F1CB48A79EA49CDD41DD3DE90EE41EC9EXMB01CMSsurr_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 SGksIHRoYW5rcyB0byBhbGwgZm9yIHRoZWlyIGhlbHBmdWwgY29tbWVudHMgb24gcHJldmlvdXMg cG9zdHMhDQoNCkkgd291bGQgbGlrZSB0byBrbm93IGlmIHRoZXJlIGFyZSBhbnkgb25saW5lIHNv dXJjZXMgb3V0IHRoZXJlIHRoYXQgZGVzY3JpYmUgaW4gYSBkaWRhY3RpYyBub24tbWF0aGVtYXRp Y2FsIHdheSBob3cgdmFyaW91cyBjb21wdXRhdGlvbmFsIGFiIGluaXRpbyBzZXF1ZW5jZXMgYXJl IGNhcmllZCBvdXQuIEVzcGVjaWFsbHksIGZvciBtdWx0aXJlZmVyZW5jZSBtZXRob2RzLiBGb3Ig ZXhhbXBsZSwgd2hhdCBleGFjdGx5IGluIEJlcm5leSBvcHRpbWl6YXRpb24gYW5kIGhvdyBkb2Vz IGlzIHdvcmsgd2l0aGluIHRoZSBzY2YgcHJvY2VkdXJlPyBJIHdvdWxkIGxvdmUgdG8gaGF2ZSBz dWNoIGEgc291cmNlIGZvciBteSBzdHVkZW50cy4NCg0KVGhhbmtzLA0KDQpCZXN0LA0KDQpQZXRl cg0KKioqU2VudCB2aWEgUm9hZFN5bmPCriBmb3IgQW5kcm9pZOKEog0K --_000_7573C7C772F1CB48A79EA49CDD41DD3DE90EE41EC9EXMB01CMSsurr_ Content-Type: text/html; charset="utf-8" Content-Transfer-Encoding: base64 PHNwYW4gc3R5bGU9ImZvbnQtc2l6ZToxMS4wcHQ7IGZvbnQtZmFtaWx5OiZxdW90O0NhbGlicmkm cXVvdDssJnF1b3Q7c2Fucy1zZXJpZiZxdW90OyI+SGksIHRoYW5rcyB0byBhbGwgZm9yIHRoZWly IGhlbHBmdWwgY29tbWVudHMgb24gcHJldmlvdXMgcG9zdHMhIDxicj48YnI+SSB3b3VsZCBsaWtl IHRvIGtub3cgaWYgdGhlcmUgYXJlIGFueSBvbmxpbmUgc291cmNlcyBvdXQgdGhlcmUgdGhhdCBk ZXNjcmliZSBpbiBhIGRpZGFjdGljIG5vbi1tYXRoZW1hdGljYWwgd2F5IGhvdyB2YXJpb3VzIGNv bXB1dGF0aW9uYWwgYWIgaW5pdGlvIHNlcXVlbmNlcyBhcmUgY2FyaWVkIG91dC4gRXNwZWNpYWxs eSwgZm9yIG11bHRpcmVmZXJlbmNlIG1ldGhvZHMuICBGb3IgZXhhbXBsZSwgd2hhdCBleGFjdGx5 IGluIEJlcm5leSBvcHRpbWl6YXRpb24gYW5kIGhvdyBkb2VzIGlzIHdvcmsgd2l0aGluIHRoZSBz Y2YgcHJvY2VkdXJlPyBJIHdvdWxkIGxvdmUgdG8gaGF2ZSBzdWNoIGEgc291cmNlIGZvciBteSBz dHVkZW50cy48YnI+PGJyPlRoYW5rcyw8YnI+IDxicj5CZXN0LDxicj48YnI+UGV0ZXI8YnI+Kioq U2VudCB2aWEgUm9hZFN5bmPCriBmb3IgQW5kcm9pZOKEojwvc3Bhbj4NCg== --_000_7573C7C772F1CB48A79EA49CDD41DD3DE90EE41EC9EXMB01CMSsurr_-- From owner-chemistry@ccl.net Mon Dec 13 09:18:00 2010 From: "miriam sgobba miriam.sgobba||gmail.com" To: CCL Subject: CCL: Prediction & Identification of protein-ligand binding sites Message-Id: <-43366-101213053439-31866-j8vfNZdFNQKVuSPJuCmdEw-*-server.ccl.net> X-Original-From: miriam sgobba Content-Type: multipart/alternative; boundary=001636c5b27dae8a2a0497483f9a Date: Mon, 13 Dec 2010 10:34:28 +0000 MIME-Version: 1.0 Sent to CCL by: miriam sgobba [miriam.sgobba . gmail.com] --001636c5b27dae8a2a0497483f9a Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Deepangi, if you know from experimental data one or more compounds that bind your protein, you can also try the blind docking technique, which allow you to perform docking simulations on large surfaces of the protein in order to ge= t unbiased mapping of the ligand. For references, see: http://www.sciencedirect.com/science?_ob=3DArticleURL&_udi=3DB6T36-4J5D6GW-= 5&_user=3D126523&_coverDate=3D02%2F20%2F2006&_rdoc=3D1&_fmt=3Dhigh&_orig=3D= search&_origin=3Dsearch&_sort=3Dd&_docanchor=3D&view=3Dc&_acct=3DC000010358= &_version=3D1&_urlVersion=3D0&_userid=3D126523&md5=3D9fb1be8e42cf768ac87b92= 1ab39d056b&searchtype=3Da http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373668/?tool=3Dpubmed and, for some blind docking applications: http://www.springerlink.com/content/p237tl40785m1tu5/ http://pubs.acs.org/doi/abs/10.1021/ci1001857 Usually, a blind docking simulation is followed by a focused docking and post-docking refinement if you want to better characterize the ligand binding mode. In my experience, a consensus among binding site identification methods (both geometrical and energetical) + blind docking technique is the best choice to identify a ligand binding site. Hope this helps! Good luck! Miriam 2010/12/12 Deepangi Pandit deepangi.pandit++gmail.com < > owner-chemistry _ ccl.net> > > >> Sent to CCL by: Deepangi Pandit [deepangi.pandit|,|gmail.com] >> Thank you Peter, for your detailed reply. I would just like to clarify >> my case based on your questions. >> >> > 1 : Do you want to apply this method on a database of proteins or just= a >> few structures? >> >> I am looking at just a few structures to identify the putative drug >> binding site. I have PDB files of protein structures (of course, >> without the compound) and have experimental data which suggests the >> compound is binding but do not know where. >> >> > 2 : Do you want to identify putative drug binding sites or whatever >> binding site a method could find (general purpose pocket prediction) >> >> I am trying to identify the putative drug binding sites not general >> purpose pocket prediction >> >> >> > 3 : Do you want to find conserved pockets among homologs? >> >> This is not my primary goal. >> >> Best, >> Deepa >> >> On Sat, Dec 11, 2010 at 4:45 PM, Peter Schmidtke >> pschmidtke[-]mmb.pcb.ub.es wrote: >> > >> > Sent to CCL by: Peter Schmidtke [pschmidtke[*]mmb.pcb.ub.es] >> > Dear Deepangi, >> > >> > protein-ligand binding site detection is a very active field and there >> > is a large variety of methods out there. >> > Since the publication of PocketPicker >> > (http://www.journal.chemistrycentral.com/content/1/1/7/abstract/) lots >> > of newer methods used the comparative table that was published with >> > PocketPicker (table 2). A very recent example is the paper by Andrea >> > Volkamer, where you have an update of this table with a few more recen= t >> > methods (http://pubs.acs.org/doi/full/10.1021/ci100241y). >> > >> > This comparison is definitely arguable, but at least it gives some hin= t >> > on general pocket prediction performance. In order to find the perfect >> > method for your purpose you should maybe clarify what is the >> > functionality your are seeking. There are lots of webservers out there= , >> > methods you have to pay and also free methods. >> > >> > Some questions that could influence your choice : >> > >> > 1 : Do you want to apply this method on a database of proteins or just= a >> > few structures? >> > 2 : Do you want to identify putative drug binding sites or whatever >> > binding site a method could find (general purpose pocket prediction) >> > 3 : Do you want to find conserved pockets among homologs? >> > >> > Concerning question 1, if you just need a method for a few structures >> > you can go for slower programs (mostly energy based algorithms) like >> > SiteMap from Schr=F6dinger (but you need a license) Q-SiteFinder or >> > PocketPicker or Vice (I think it's sold by Tripos) There are surely mo= re >> > than that. >> > If you need to process a large number of structures, considering >> > geometry based methods might become an interesting choice. Choices cou= ld >> > be Ligsite, fpocket, PASS, SiteFinder (included in MOE by CCG) ... >> > >> > Regarding question 2. Pocket prediction is not equal drug binding site >> > prediction. Recent druggability prediction methods have been published >> > and some scores are available ready for use in SiteMap (I don't know i= f >> > you still have to calculate it or if they finally included it into the >> > SiteMap distribution) and fpocket. I suspect also QSiteFinder might gi= ve >> > indications on druggability (I extrapolate from the methodology I just >> > read very quickly, so maybe I'm wrong here ;) ). >> > >> > Regarding question 3, I think ligsite csc can help there >> > (http://projects.biotec.tu-dresden.de/pocket/), or else hpocket, which >> > is part of the fpocket webserver : >> > http://bioserv.rpbs.univ-paris-diderot.fr/fpocket/ >> > >> > I hope that this gives you at least a direction, there are really lots >> > of methods and it is indeed not easy to know which one to use ;) >> > >> > Ah, I nearly forgot, metapocket2.0 is a sort of consensus pocket >> > prediction method that makes use of LIGSITEcsc, PASS, Q-SiteFinder, >> > SURFNET, Fpocket, GHECOM and ConCavity. This has again advantages and >> > disadvantages, but well, at least you know that it exists ;) >> > >> > Good luck. >> > >> > Peter Schmidtke >> > >> > >> > >> > >> > On 12/11/2010 06:44 PM, Deepangi Pandit deepangi.pandit~!~gmail.comwro= te: >> >> Sent to CCL by: Deepangi Pandit [deepangi.pandit(!)gmail.com] >> >> Dear All: >> >> I tried to search literature and Internet to find a reliable method >> >> that I can use to identify protein-ligand binding site. I came across >> >> number of papers but I am unable to evaluate the methods before I >> >> start using them. I was also unable to find a review which compares >> >> the methods. It seems method can be broadly classified as "Geometry >> >> based" and "Energy Based". Could you please recommend from your own >> >> experience which method gives reasonable results. Also, feel free to >> >> share pros and cons of the method. >> >> >> >> Thank you. >> >> Deepa >> >> >> >> List of methods I came across >> >> >> >> Q-Site Finder >> >> http://www.bioinformatics.leeds.ac.uk/qsitefinder >> >> >> >> Surface triplet propensities >> >> http://opus.bch.ed.ac.uk/stp >> >> >> >> Screen >> >> http://interface.bioc.columbia.edu/screen> >> > >> > >> >> >> >> -=3D This is automatically added to each message by the mailing script = =3D->> >> >> > --001636c5b27dae8a2a0497483f9a Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Deepangi,

if you know from experimental data one or more=20 compounds that bind your protein, you can also try the blind docking=20 technique, which allow you to perform docking simulations on large=20 surfaces of the protein in order to get unbiased mapping of the ligand. For references, see:
http:= //www.sciencedirect.com/science?_ob=3DArticleURL&_udi=3DB6T36-4J5D6GW-5= &_user=3D126523&_coverDate=3D02%2F20%2F2006&_rdoc=3D1&_fmt= =3Dhigh&_orig=3Dsearch&_origin=3Dsearch&_sort=3Dd&_docancho= r=3D&view=3Dc&_acct=3DC000010358&_version=3D1&_urlVersion= =3D0&_userid=3D126523&md5=3D9fb1be8e42cf768ac87b921ab39d056b&se= archtype=3Da

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC23736= 68/?tool=3Dpubmed

and, for some blind docking applications:
<= br> http://www.springerlink.com/content/p237tl40785m1tu5/
http://pubs.acs.org/doi/abs/10.1021/ci1001857

Usually, a blind docking simulation is followed by a focused docking and=20 post-docking refinement if you want to better characterize
the ligand binding mode.
In my experience, a consensus among binding=20 site identification methods (both geometrical and energetical) + blind=20 docking technique is the best choice to identify a ligand binding=20 site.

Hope this helps!
Good luck!

Miriam


2010/12/12 Deepangi Pandit deepangi.pandit++gmail.com = <owner-chem= istry _ ccl.net>


Sent to CCL by: Deepangi Pandit [deepangi.pandit|,|gmail.com]
Thank you Peter, for your detailed reply. I would just like to clarify
my case based on your questions.

> 1 : Do you want to apply this method on a database of proteins or just= a few structures?

I am looking at just a few structures to identify the putative drug
binding site. I have PDB files of protein structures (of course,
without the compound) and have experimental data which suggests the
compound is binding but do not know where.

> 2 : Do you want to identify putative drug binding sites or whatever bi= nding site a method could find (general purpose pocket prediction)

I am trying to identify the putative drug binding sites not general
purpose pocket prediction


> 3 : Do you want to find conserved pockets among homologs?

This is not my primary goal.

Best,
Deepa

On Sat, Dec 11, 2010 at 4:45 PM, Peter Schmidtke
pschmidtke[-]mmb.pcb.ub.= es <owner-chemistry|-|c= cl.net> wrote:
>
> Sent to CCL by: Peter Schmidtke [pschmidtke[*]mmb.pcb.ub.es]
> Dear Deepangi,
>
> protein-ligand binding site detection is a very active field and there=
> is a large variety of methods out there.
> Since the publication of PocketPicker
> (http://www.journal.chemistrycentral.com/content/1/= 1/7/abstract/) lots
> of newer methods used the comparative table that was published with > PocketPicker (table 2). A very recent example is the paper by Andrea > Volkamer, where you have an update of this table with a few more recen= t
> methods (http://pubs.acs.org/doi/full/10.1021/ci100241y).
>
> This comparison is definitely arguable, but at least it gives some hin= t
> on general pocket prediction performance. In order to find the perfect=
> method for your purpose you should maybe clarify what is the
> functionality your are seeking. There are lots of webservers out there= ,
> methods you have to pay and also free methods.
>
> Some questions that could influence your choice :
>
> 1 : Do you want to apply this method on a database of proteins or just= a
> few structures?
> 2 : Do you want to identify putative drug binding sites or whatever > binding site a method could find (general purpose pocket prediction) > 3 : Do you want to find conserved pockets among homologs?
>
> Concerning question 1, if you just need a method for a few structures<= br> > you can go for slower programs (mostly energy based algorithms) like > SiteMap from Schr=F6dinger (but you need a license) Q-SiteFinder or > PocketPicker or Vice (I think it's sold by Tripos) There are surel= y more
> than that.
> If you need to process a large number of structures, considering
> geometry based methods might become an interesting choice. Choices cou= ld
> be Ligsite, fpocket, PASS, SiteFinder (included in MOE by CCG) ...
>
> Regarding question 2. Pocket prediction is not equal drug binding site=
> prediction. Recent druggability prediction methods have been published=
> and some scores are available ready for use in SiteMap (I don't kn= ow if
> you still have to calculate it or if they finally included it into the=
> SiteMap distribution) and fpocket. I suspect also QSiteFinder might gi= ve
> indications on druggability (I extrapolate from the methodology I just=
> read very quickly, so maybe I'm wrong here ;) ).
>
> Regarding question 3, I think ligsite csc can help there
> (http://projects.biotec.tu-dresden.de/pocket/), or else hpocket, w= hich
> is part of the fpocket webserver :
> http://bioserv.rpbs.univ-paris-diderot.fr/fpocket/
>
> I hope that this gives you at least a direction, there are really lots=
> of methods and it is indeed not easy to know which one to use ;)
>
> Ah, I nearly forgot, metapocket2.0 is a sort of consensus pocket
> prediction method that makes use of LIGSITEcsc, PASS, Q-SiteFinder, > SURFNET, Fpocket, GHECOM and ConCavity. This has again advantages and<= br> > disadvantages, but well, at least you know that it exists ;)
>
> Good luck.
>
> Peter Schmidtke
>
>
>
>
> On 12/11/2010 06:44 PM, Deepangi Pandit deepangi.pandit~!~gmail.com wrote:
>> Sent to CCL by: Deepangi Pandit [deepangi.pandit(!)gmail.com]
>> Dear All:
>> I tried to search literature and Internet to find a reliable metho= d
>> that I can use to identify protein-ligand binding site. I came acr= oss
>> number of papers but I am unable to evaluate the methods before I<= br> >> start using them. I was also unable to find a review which compare= s
>> the methods. It seems method can be broadly classified as "Ge= ometry
>> based" and "Energy Based". Could you please recomme= nd from your own
>> experience which method gives reasonable results. Also, feel free = to
>> share pros and cons of the method.
>>
>> Thank you.
>> Deepa
>>
>> List of methods I came across
>>
>> Q-Site Finder
>> http://www.bioinformatics.leeds.ac.uk/qsitefinder
>>
>> Surface triplet propensities
>> http://= opus.bch.ed.ac.uk/stp
>>
>> Screen
>> http://interface.bioc.columbia.edu/screen> =A0 =A0 =A0http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://ww= w.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.ne= t/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> >
>



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY _ ccl.net or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST _ ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/




--001636c5b27dae8a2a0497483f9a-- From owner-chemistry@ccl.net Mon Dec 13 09:53:00 2010 From: "Michel Petitjean petitjean.chiral[*]gmail.com" To: CCL Subject: CCL: software for selective alignment of different elements of the small molecules Message-Id: <-43367-101213063324-29898-I4C9u9aIYJMTTMfvIPc4QA:server.ccl.net> X-Original-From: Michel Petitjean Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 13 Dec 2010 12:33:17 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral:-:gmail.com] Dear Andrew, May I recommend you the following procedure, with the help of the CSR freeware (http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html) You have two molecules (1 and 2), and you want to force the molecule 2 to have a part aligned on a fixed part of molecule1. (1) Extract the fixed part of molecule 1 and store it in a file, and consider it as being your new molecule 1. (2) Store molecule 2 in the same file as the new molecule 1. (3) Align with CSR the molecule 2 (which is moved), on the new molecule 1: CSR stores the aligned image of molecule 2 on your molecule 1 in a separate mol file, and outputs the optimal rotation-translation of the alignment. Now, you have both the mole files of the full original molecule 1 and the aligned molecule 2, with alignment made on the basis of the part you extracted in mol.1 Hope it helps. Michel. 2010/12/11 Andrew Voronkov drugdesign*yandex.ru : > > Sent to CCL by: Andrew Voronkov [drugdesign-x-yandex.ru] > > Dear CCL users, > I'd like to find the software for alignment of the selected  small molecule elements. For example I have a series of conformations and I am getting alignment with one shared element, while I'd like to try to use another. Let's say I have parts A, B, C, D and E and I want to get parts D and E alignmed so that I can see the differences in parts A and B orientation. Can you please recommend software packages which can help me to do selective alignment? > > It would be nice to use something free or with evaluation version. > > > > Sincerely yours, > Andrey > From owner-chemistry@ccl.net Mon Dec 13 10:28:00 2010 From: "Jean Jules FIFEN julesfifen||gmail.com" To: CCL Subject: CCL:G: Relaxed surface scan with frequencies at each point Message-Id: <-43368-101213090857-3315-tbMh1eYYLKJJr8W22dUFcg^_^server.ccl.net> X-Original-From: Jean Jules FIFEN Content-Type: multipart/alternative; boundary=00163646dace302d0e04974b3eae Date: Mon, 13 Dec 2010 15:08:48 +0100 MIME-Version: 1.0 Sent to CCL by: Jean Jules FIFEN [julesfifen**gmail.com] --00163646dace302d0e04974b3eae Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear J. Bredenbeck, It is clear, you are right. To do what you are expecting, I think that you can do opt freq job at each point by freezing the corresponding coordinate. So, if you need n steps during your scan, you would built n input files. Each file should be related to a specific value of the coordinate to be scanned. Input file should look as: ***************************************************************************= *********************** # opt=3Dmodredundant freq ... title charge spin geometry specification D 1 8 14 15 20.000000 F ***************************************************************************= *********************** if the interresting coordinate is the dihedral angle formed by atoms 1, 8, 14 and 15 and it value is frozen to 20.0=B0. Obviously, the drawback of thi= s procedure is that it becomes painful as n increases. You can also do the same thing putting all requested jobs in the same input file using --Link1---, retrieving geometry from the previous job and modify the value of the frozen coordinate. For example, ***************************************************************************= *********************** %chk=3Dtest # opt=3Dmodredundant freq ... title charge spin geometry specification D 1 8 14 15 20.000000 F --Link1-- %chk=3Dtest # opt=3Dmodredundant freq guess=3Dread geom=3Dallcheck ... D 1 8 14 15 40.000000 F --Link1-- %chk=3Dtest # opt=3Dmodredundant freq guess=3Dread geom=3Dallcheck ... D 1 8 14 15 60.000000 F and so forth... ***************************************************************************= *********************** I have never try the latter method but I think it is logic. You can also tr= y it. On 13 December 2010 11:08, Jens Bredenbeck jbreden _ gmx.de < owner-chemistry ~ ccl.net> wrote: > > Sent to CCL by: "Jens Bredenbeck" [jbreden]=3D[gmx.de] > Dear J. Jules, > > thanks for the reply. Unfortunatley this choice of keywords > (opt=3Dmodredundant freq) does not result in a frequency calculation for = every > point of the surface scan but just in a frequency calculation for the las= t > point of the surface scan. > > Best regards > J. Bredenbeck > > > The keywords to use are: *opt=3Dmodredundant freq. *Obviously, don't fo= rget > > to specify coordinates which should be scanned as it would be done in = a > > rigid scan. For further explanations, read gaussian manual. > > > > J. Jules. > > > > On 10 December 2010 22:37, J Bredenbeck jbreden[#]gmx.de < > > owner-chemistry^^ccl.net> wrote: > > > > > > > > Sent to CCL by: "J Bredenbeck" [jbreden!=3D!gmx.de] > > > Dear CCL Users, > > > > > > I would like to do a relaxed surface scan in Gaussian03 with a normal > > mode > > > calculation at each point after optimization. I would be great if > > somebody > > > could tell me how this type of calculation can be set up. > > > > > > Regards, > > > Jens> > > > > > > > > > > > > -- > > J. Jules. > > -- > Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief! > Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 J. Jules. --00163646dace302d0e04974b3eae Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear J. Bredenbeck,

It is clear, you are right. To = do what you are expecting, I think that you can do opt freq job at each poi= nt by freezing the corresponding coordinate. So, if you need n steps during= your scan, you would built n input files. Each file should be related to a= specific value of the coordinate to be scanned.=A0 Input file should look = as:

***********************************************************************= ***************************
# opt=3Dmodredundant freq ...

title<= br>
charge spin
geometry specification

D 1 8 14 15 20.000000 F=

***********************************************************************= ***************************
if the interresting coordinate is the dihedr= al angle formed by atoms 1, 8, 14 and 15 and it value is frozen to 20.0=B0.= Obviously, the drawback of this procedure is that it becomes painful as n = increases. You can also do the same thing putting all requested jobs in the= same input file using --Link1---, retrieving geometry from the previous jo= b and modify the value of the frozen coordinate.
For example,
***********************************************************= ***************************************
%chk=3Dtest
# opt=3Dmodredundant freq ...

title

charge spin
geometry specification

D 1 8 14 15 20.000000 F

--Link1--
%chk=3Dtest
# opt=3Dmodredundant freq guess=3Dread geom=3Dallcheck ...

D 1 8 14 = 15 40.000000 F

--Link1--
%chk=3Dtest
# opt=3Dmodredundant freq guess=3Dread geom=3Dallcheck ...

D 1 8 14 15 60.000000 F

and so forth...

***************************************************************************= ***********************
I have never try the latter method but I think i= t is logic. You can also try it.


On 1= 3 December 2010 11:08, Jens Bredenbeck jbreden _ = gmx.de <owner-chemistry ~ ccl.net> wrote:

Sent to CCL by: "Jens Bredenbeck" [jbreden]=3D[gmx.de]
Dear J. Jules,

thanks for the reply. Unfortunatley this choice of keywords (opt=3Dmodredun= dant freq) does not result in a frequency calculation for every point of th= e surface scan but just in a frequency calculation for the last point of th= e surface scan.

Best regards
J. Bredenbeck

> The keywords to use are: *opt=3Dmodredundant freq. *Obviously, don'= ;t forget
> to =A0specify coordinates which should be scanned as it would be done = in a
> rigid scan. For further explanations, read gaussian manual.
>
> J. Jules.
>
> On 10 December 2010 22:37, J Bredenbeck jbreden[#]gmx.de <
> owner-chemistry^^ccl.net<= /a>> wrote:
>
> >
> > Sent to CCL by: "J =A0Bredenbeck" [jbreden!=3D!gmx.de]
> > Dear CCL Users,
> >
> > I would like to do a relaxed surface scan in Gaussian03 with a no= rmal
> mode
> > calculation at each point after optimization. I would be great if=
> somebody
> > could tell me how this type of calculation can be set up.
> >
> > Regards,
> > Jens>
> >
> >
>
>
> --
> J. Jules.

--
Neu: GMX De-Mail - Einfach wie E-Mail, sicher wie ein Brief!
Jetzt De-Mail-Adresse reservieren: http://portal.gmx.net/de/go/demail



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY ~ ccl.n= et or use:
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEM= ISTRY-REQUEST ~ ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.n= et/jobs
Conferences: http://server.ccl.net/chemistry/announcements/co= nferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml
=A0 =A0 =A0h= ttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/





--
J. Jul= es.

--00163646dace302d0e04974b3eae-- From owner-chemistry@ccl.net Mon Dec 13 11:04:00 2010 From: "Peter Schmidtke pschmidtke^^^mmb.pcb.ub.es" To: CCL Subject: CCL: Prediction & Identification of protein-ligand binding sites Message-Id: <-43369-101213104649-22802-i/kfCa5cD/vluDe5p8mvbw|-|server.ccl.net> X-Original-From: Peter Schmidtke Content-Type: multipart/alternative; boundary=Apple-Mail-1-415370384 Date: Mon, 13 Dec 2010 16:46:22 +0100 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Peter Schmidtke [pschmidtke ~ mmb.pcb.ub.es] --Apple-Mail-1-415370384 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=iso-8859-1 Very good point. However, one has to bear in mind that despite the fact = that docking software can produce reasonable poses, the scoring schemes = are still not reliable enough. So as you said, a consensus prediction = between docking and pocket prediction can give hints. But there again = it's not proof.=20 Ideally, from the output of the previous two analyses you could run MD = simulations then with your ligand docked into the pocket to see if it is = stable...which is obviously a lot heavier, but certainly less than = trying to get a crystal structure ;) On 13/12/2010, at 11:34, miriam sgobba miriam.sgobba||gmail.com wrote: > Dear Deepangi, >=20 > if you know from experimental data one or more compounds that bind = your protein, you can also try the blind docking technique, which allow = you to perform docking simulations on large surfaces of the protein in = order to get unbiased mapping of the ligand.=20 > For references, see: > = http://www.sciencedirect.com/science?_ob=3DArticleURL&_udi=3DB6T36-4J5D6GW= -5&_user=3D126523&_coverDate=3D02%2F20%2F2006&_rdoc=3D1&_fmt=3Dhigh&_orig=3D= search&_origin=3Dsearch&_sort=3Dd&_docanchor=3D&view=3Dc&_acct=3DC00001035= 8&_version=3D1&_urlVersion=3D0&_userid=3D126523&md5=3D9fb1be8e42cf768ac87b= 921ab39d056b&searchtype=3Da >=20 > http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373668/?tool=3Dpubmed >=20 > and, for some blind docking applications: >=20 > http://www.springerlink.com/content/p237tl40785m1tu5/ > http://pubs.acs.org/doi/abs/10.1021/ci1001857 >=20 > Usually, a blind docking simulation is followed by a focused docking = and post-docking refinement if you want to better characterize > the ligand binding mode. > In my experience, a consensus among binding site identification = methods (both geometrical and energetical) + blind docking technique is = the best choice to identify a ligand binding site.=20 >=20 > Hope this helps! > Good luck! >=20 > Miriam >=20 >=20 > 2010/12/12 Deepangi Pandit deepangi.pandit++gmail.com = >=20 >=20 > Sent to CCL by: Deepangi Pandit [deepangi.pandit|,|gmail.com] > Thank you Peter, for your detailed reply. I would just like to clarify > my case based on your questions. >=20 > > 1 : Do you want to apply this method on a database of proteins or = just a few structures? >=20 > I am looking at just a few structures to identify the putative drug > binding site. I have PDB files of protein structures (of course, > without the compound) and have experimental data which suggests the > compound is binding but do not know where. >=20 > > 2 : Do you want to identify putative drug binding sites or whatever = binding site a method could find (general purpose pocket prediction) >=20 > I am trying to identify the putative drug binding sites not general > purpose pocket prediction >=20 >=20 > > 3 : Do you want to find conserved pockets among homologs? >=20 > This is not my primary goal. >=20 > Best, > Deepa >=20 > On Sat, Dec 11, 2010 at 4:45 PM, Peter Schmidtke > pschmidtke[-]mmb.pcb.ub.es wrote: > > > > Sent to CCL by: Peter Schmidtke [pschmidtke[*]mmb.pcb.ub.es] > > Dear Deepangi, > > > > protein-ligand binding site detection is a very active field and = there > > is a large variety of methods out there. > > Since the publication of PocketPicker > > (http://www.journal.chemistrycentral.com/content/1/1/7/abstract/) = lots > > of newer methods used the comparative table that was published with > > PocketPicker (table 2). A very recent example is the paper by Andrea > > Volkamer, where you have an update of this table with a few more = recent > > methods (http://pubs.acs.org/doi/full/10.1021/ci100241y). > > > > This comparison is definitely arguable, but at least it gives some = hint > > on general pocket prediction performance. In order to find the = perfect > > method for your purpose you should maybe clarify what is the > > functionality your are seeking. There are lots of webservers out = there, > > methods you have to pay and also free methods. > > > > Some questions that could influence your choice : > > > > 1 : Do you want to apply this method on a database of proteins or = just a > > few structures? > > 2 : Do you want to identify putative drug binding sites or whatever > > binding site a method could find (general purpose pocket prediction) > > 3 : Do you want to find conserved pockets among homologs? > > > > Concerning question 1, if you just need a method for a few = structures > > you can go for slower programs (mostly energy based algorithms) like > > SiteMap from Schr=F6dinger (but you need a license) Q-SiteFinder or > > PocketPicker or Vice (I think it's sold by Tripos) There are surely = more > > than that. > > If you need to process a large number of structures, considering > > geometry based methods might become an interesting choice. Choices = could > > be Ligsite, fpocket, PASS, SiteFinder (included in MOE by CCG) ... > > > > Regarding question 2. Pocket prediction is not equal drug binding = site > > prediction. Recent druggability prediction methods have been = published > > and some scores are available ready for use in SiteMap (I don't know = if > > you still have to calculate it or if they finally included it into = the > > SiteMap distribution) and fpocket. I suspect also QSiteFinder might = give > > indications on druggability (I extrapolate from the methodology I = just > > read very quickly, so maybe I'm wrong here ;) ). > > > > Regarding question 3, I think ligsite csc can help there > > (http://projects.biotec.tu-dresden.de/pocket/), or else hpocket, = which > > is part of the fpocket webserver : > > http://bioserv.rpbs.univ-paris-diderot.fr/fpocket/ > > > > I hope that this gives you at least a direction, there are really = lots > > of methods and it is indeed not easy to know which one to use ;) > > > > Ah, I nearly forgot, metapocket2.0 is a sort of consensus pocket > > prediction method that makes use of LIGSITEcsc, PASS, Q-SiteFinder, > > SURFNET, Fpocket, GHECOM and ConCavity. This has again advantages = and > > disadvantages, but well, at least you know that it exists ;) > > > > Good luck. > > > > Peter Schmidtke > > > > > > > > > > On 12/11/2010 06:44 PM, Deepangi Pandit deepangi.pandit~!~gmail.com = wrote: > >> Sent to CCL by: Deepangi Pandit [deepangi.pandit(!)gmail.com] > >> Dear All: > >> I tried to search literature and Internet to find a reliable method > >> that I can use to identify protein-ligand binding site. I came = across > >> number of papers but I am unable to evaluate the methods before I > >> start using them. I was also unable to find a review which compares > >> the methods. It seems method can be broadly classified as "Geometry > >> based" and "Energy Based". Could you please recommend from your own > >> experience which method gives reasonable results. Also, feel free = to > >> share pros and cons of the method. > >> > >> Thank you. > >> Deepa > >> > >> List of methods I came across > >> > >> Q-Site Finder > >> http://www.bioinformatics.leeds.ac.uk/qsitefinder > >> > >> Surface triplet propensities > >> http://opus.bch.ed.ac.uk/stp > >> > >> Screen > >> http://interface.bioc.columbia.edu/screen> => => => => > > > > >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script = =3D- >=20 >=20 >=20 > E-mail to subscribers: CHEMISTRY#,#ccl.net or use:>=20 > E-mail to administrators: CHEMISTRY-REQUEST#,#ccl.net or use>=20>=20>=20> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20 >=20>=20>=20 >=20 >=20 >=20 Peter Schmidtke ----------------- PhD Student Department of Physical Chemistry School of Pharmacy University of Barcelona Barcelona, Spain --Apple-Mail-1-415370384 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=iso-8859-1 Very = good point. However, one has to bear in mind that despite the fact that = docking software can produce reasonable poses, the scoring schemes are = still not reliable enough. So as you said, a consensus prediction = between docking and pocket prediction can give hints. But there again = it's not proof. 

Ideally, from the output of the = previous two analyses you could run MD simulations then with your ligand = docked into the pocket to see if it is stable...which is obviously a lot = heavier, but certainly less than trying to get a crystal structure = ;)


On 13/12/2010, at 11:34, = miriam sgobba miriam.sgobba||gmail.com wrote:

Dear = Deepangi,

if you know from experimental data one or more=20 compounds that bind your protein, you can also try the blind docking=20 technique, which allow you to perform docking simulations on large=20 surfaces of the protein in order to get unbiased mapping of the ligand. =
For references, see:
http://www.sciencedirect.com/science?_ob=3DArticleURL&am= p;_udi=3DB6T36-4J5D6GW-5&_user=3D126523&_coverDate=3D02%2F20%2F200= 6&_rdoc=3D1&_fmt=3Dhigh&_orig=3Dsearch&_origin=3Dsearch&am= p;_sort=3Dd&_docanchor=3D&view=3Dc&_acct=3DC000010358&_ver= sion=3D1&_urlVersion=3D0&_userid=3D126523&md5=3D9fb1be8e42cf76= 8ac87b921ab39d056b&searchtype=3Da

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373668/?too= l=3Dpubmed

and, for some blind docking applications:

http://www.springerlink.com/content/p237tl40785m1tu5/
http://pubs.acs.org/doi/abs/10.1021/ci1001857
Usually, a blind docking simulation is followed by a focused docking and=20 post-docking refinement if you want to better characterize
the ligand binding mode.
In my experience, a consensus among binding=20= site identification methods (both geometrical and energetical) + blind=20= docking technique is the best choice to identify a ligand binding=20 site.

Hope this helps!
Good luck!

Miriam


2010/12/12 Deepangi Pandit = deepangi.pandit++gmail.com <owner-chemistry#,#ccl.net>


Sent to CCL by: Deepangi Pandit [deepangi.pandit|,|gmail.com]
Thank you Peter, for your detailed reply. I would just like to = clarify
my case based on your questions.

> 1 : Do you want to apply this method on a database of proteins or = just a few structures?

I am looking at just a few structures to identify the putative drug
binding site. I have PDB files of protein structures (of course,
without the compound) and have experimental data which suggests the
compound is binding but do not know where.

> 2 : Do you want to identify putative drug binding sites or whatever = binding site a method could find (general purpose pocket prediction)

I am trying to identify the putative drug binding sites not general
purpose pocket prediction


> 3 : Do you want to find conserved pockets among homologs?

This is not my primary goal.

Best,
Deepa

On Sat, Dec 11, 2010 at 4:45 PM, Peter Schmidtke
pschmidtke[-]mmb.pcb.ub.es <owner-chemistry|-|ccl.net> wrote:
>
> Sent to CCL by: Peter Schmidtke [pschmidtke[*]mmb.pcb.ub.es]
> Dear Deepangi,
>
> protein-ligand binding site detection is a very active field and = there
> is a large variety of methods out there.
> Since the publication of PocketPicker
> (http://www.journal.chemistrycentral.com/content/1/1/7/ab= stract/) lots
> of newer methods used the comparative table that was published = with
> PocketPicker (table 2). A very recent example is the paper by = Andrea
> Volkamer, where you have an update of this table with a few more = recent
> methods (http://pubs.acs.org/doi/full/10.1021/ci100241y).
= >
> This comparison is definitely arguable, but at least it gives some = hint
> on general pocket prediction performance. In order to find the = perfect
> method for your purpose you should maybe clarify what is the
> functionality your are seeking. There are lots of webservers out = there,
> methods you have to pay and also free methods.
>
> Some questions that could influence your choice :
>
> 1 : Do you want to apply this method on a database of proteins or = just a
> few structures?
> 2 : Do you want to identify putative drug binding sites or = whatever
> binding site a method could find (general purpose pocket = prediction)
> 3 : Do you want to find conserved pockets among homologs?
>
> Concerning question 1, if you just need a method for a few = structures
> you can go for slower programs (mostly energy based algorithms) = like
> SiteMap from Schr=F6dinger (but you need a license) Q-SiteFinder = or
> PocketPicker or Vice (I think it's sold by Tripos) There are surely = more
> than that.
> If you need to process a large number of structures, = considering
> geometry based methods might become an interesting choice. Choices = could
> be Ligsite, fpocket, PASS, SiteFinder (included in MOE by CCG) = ...
>
> Regarding question 2. Pocket prediction is not equal drug binding = site
> prediction. Recent druggability prediction methods have been = published
> and some scores are available ready for use in SiteMap (I don't = know if
> you still have to calculate it or if they finally included it into = the
> SiteMap distribution) and fpocket. I suspect also QSiteFinder might = give
> indications on druggability (I extrapolate from the methodology I = just
> read very quickly, so maybe I'm wrong here ;) ).
>
> Regarding question 3, I think ligsite csc can help there
> (http://projects.biotec.tu-dresden.de/pocket/), or = else hpocket, which
> is part of the fpocket webserver :
> http://bioserv.rpbs.univ-paris-diderot.fr/fpocket/ >
> I hope that this gives you at least a direction, there are really = lots
> of methods and it is indeed not easy to know which one to use = ;)
>
> Ah, I nearly forgot, metapocket2.0 is a sort of consensus = pocket
> prediction method that makes use of LIGSITEcsc, PASS, = Q-SiteFinder,
> SURFNET, Fpocket, GHECOM and ConCavity. This has again advantages = and
> disadvantages, but well, at least you know that it exists ;)
>
> Good luck.
>
> Peter Schmidtke
>
>
>
>
> On 12/11/2010 06:44 PM, Deepangi Pandit deepangi.pandit~!~gmail.com wrote:
>> Sent to CCL by: Deepangi Pandit [deepangi.pandit(!)gmail.com]
>> Dear All:
>> I tried to search literature and Internet to find a reliable = method
>> that I can use to identify protein-ligand binding site. I came = across
>> number of papers but I am unable to evaluate the methods before = I
>> start using them. I was also unable to find a review which = compares
>> the methods. It seems method can be broadly classified as = "Geometry
>> based" and "Energy Based". Could you please recommend from your = own
>> experience which method gives reasonable results. Also, feel = free to
>> share pros and cons of the method.
>>
>> Thank you.
>> Deepa
>>
>> List of methods I came across
>>
>> Q-Site Finder
>> http://www.bioinformatics.leeds.ac.uk/qsitefinder >>
>> Surface triplet propensities
>> http://opus.bch.ed.ac.uk/stp
>>
>> Screen
>> http://interface.bioc.columbia.edu/screen> =      http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =      http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =      http://www.ccl.net/chemistry/sub_unsub.shtml> =      http://www.ccl.net/spammers.txt>
>
>



-=3D This is automatically added to each message by the mailing script = =3D-



E-mail to subscribers: CHEMISTRY#,#ccl.net or use:
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST#,#ccl.net or use
     http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
     http://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs
Conferences: http://server.ccl.net/chemistry/announcements/conference= s/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtml

     http://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/<= br>




Peter = Schmidtke

-----------------
PhD = Student
Department of Physical Chemistry
School of = Pharmacy
University of Barcelona
Barcelona, = Spain

= --Apple-Mail-1-415370384-- From owner-chemistry@ccl.net Mon Dec 13 11:39:00 2010 From: "Mikael Johansson mikael.johansson*iki.fi" To: CCL Subject: CCL: Queries on DFT functional Message-Id: <-43370-101213103200-7214-cIJXanajna8XTEPZRTYTjQ{=}server.ccl.net> X-Original-From: Mikael Johansson Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII Date: Mon, 13 Dec 2010 17:31:50 +0200 (EET) MIME-Version: 1.0 Sent to CCL by: Mikael Johansson [mikael.johansson||iki.fi] Hello! On Sun, 12 Dec 2010, Eli Lam elizabeth.shlam-,-gmail.com wrote: > more percentage of HF may shift the entire absorption spectrum back to > the correct wavelength. So is it HF, which has neglect the electron > correlation, will always shift the spectrum to the shorter wavelength? In addition to the interesting analysis by Ulf, which I didn't think of, one typical reason for this is the self-interaction error present in most non-hybrid functionals. When you add HF exchange, the amount of SIE is reduced, resulting in a stabilisation of the occupied orbitals, thus increasing the gap between occupieds and virtuals, leading to more energetic transitions, that is, shorter wavelengths. There is a lot of literature on why and when DFT fails for excitations, google knows. Have a nice day, Mikael J. http://www.iki.fi/~mpjohans/ From owner-chemistry@ccl.net Mon Dec 13 12:14:00 2010 From: "Eli Lam elizabeth.shlam::gmail.com" To: CCL Subject: CCL: Queries on DFT functional Message-Id: <-43371-101213110348-16535-lDls7mi3bYSeIK4EXavV2A^^^server.ccl.net> X-Original-From: "Eli Lam" Date: Mon, 13 Dec 2010 11:03:47 -0500 Sent to CCL by: "Eli Lam" [elizabeth.shlam^-^gmail.com] Thanks so much for your help! Actually I've run the TDDFT using PBE1PBE functional for a donor-acceptor molecule. However, it seems the lowest absorption band is much red shifted than the experimental one. I've learnt that since HF may blue shift the energy, I could add more portion of HF in the route for calculations. However, it confuses me on how to choose the optimal portion of HF in calculations and how to implant some HF in the PBE1PBE functional... Would you please advise? Thank you so much!! Sincerely, Eli > "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek!=!few.vu.nl" wrote: > > Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek-,-few.vu.nl] > > I would like to ask why is neglecting electron correlation can shift the absorption > > spectrum? > > This is for almost purely "mathematical" reasons. In HF the orbitals > are optimized for the ground state. Any "relaxation" of the orbitals > that would happen during excitation is then neglected, because such > relaxation comes from doubly and higher excited determinants. The > excited state energy is thus computed using non-optimal orbitals, and > will therefore be higher than the lowest possible HF energy for the > excited state. This is in turn higher than the real excited state > energy. However, the neglect of orbital relaxation is the largest > error in TDHF. Methods such as CIS(D) or the static exchange > approximation (for core excitations) try to fix this error. > > Sincerely, > Ulf Ekstrom > > From owner-chemistry@ccl.net Mon Dec 13 12:48:00 2010 From: "Roy Jensen JensenRH%MacEwan.ca" To: CCL Subject: CCL:G: Relaxed surface scan with frequencies at each point Message-Id: <-43372-101213123309-21125-XC+3ew/QZ+LMYx6S2jxCuQ(a)server.ccl.net> X-Original-From: Roy Jensen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 13 Dec 2010 10:32:38 -0700 MIME-Version: 1.0 Sent to CCL by: Roy Jensen [JensenRH-*-MacEwan.ca] A few years ago, I customized my own route card to calculate a full and NBO population analysis after each step. With the aid of the Gaussian manual on IOPs and several test runs, it should be as simple as inserting the IOPs for a frequency run after each optimization and before it loops. ! The non-standard route is equivalent to: ! #P UB3LYP/6-311++G(d,p) 5D opt(z-matrix,maxcycle=10) nosymm ! pop(full,NBO) IOP(1/7=60,2/16=3,2/9=222,5/13=1) ! Except there is a full and NBO population analysis after each step. #P nonstd 1/6=10,7=60,10=7,14=-1,18=40,26=3,38=1/1,3; 2/9=222,15=1,16=3,17=6,18=5,40=1/2; 3/5=4,6=6,7=1111,8=1,11=2,25=1,30=1/1,2,3; 4/7=2/1; 5/5=2,13=1,38=4,42=-5/2; 6/7=3,28=1/1,7; 7/29=1,30=1/1,2,3,16; 1/6=10,7=60,10=7,14=-1,18=40/3(1); 99//99; 2/9=222,15=1,16=3/2; 3/5=4,6=6,7=1111,8=1,11=2,25=1,30=1/1,2,3; 4/5=5,7=2,16=2/1; 5/5=2,13=1,38=4,42=-5/2; 7/30=1/1,2,3,16; 6/7=3,28=1/1,7; 1/6=10,7=60,14=-1,18=40/3(-6); 2/9=222,15=1,16=3/2; 6/7=3,19=2,28=1/1,7; 99/9=1/99; Dr. Roy Jensen (==========)-----------------------------------------¤ Chemistry, Grant MacEwan University Room 5-172J, 10700-104 Avenue Edmonton, AB T5J 4S2 780.633.3915 On Mon, 13 Dec 2010 11:08:15 +0100, you wrote: > >Sent to CCL by: "Jens Bredenbeck" [jbreden]=[gmx.de] >Dear J. Jules, > >thanks for the reply. Unfortunatley this choice of keywords (opt=modredundant freq) does not result in a frequency calculation for every point of the surface scan but just in a frequency calculation for the last point of the surface scan. > >Best regards >J. Bredenbeck > >> The keywords to use are: *opt=modredundant freq. *Obviously, don't forget >> to specify coordinates which should be scanned as it would be done in a >> rigid scan. For further explanations, read gaussian manual. >> >> J. Jules. >> >> On 10 December 2010 22:37, J Bredenbeck jbreden[#]gmx.de < >> owner-chemistry^^ccl.net> wrote: >> >> > >> > Sent to CCL by: "J Bredenbeck" [jbreden!=!gmx.de] >> > Dear CCL Users, >> > >> > I would like to do a relaxed surface scan in Gaussian03 with a normal >> mode >> > calculation at each point after optimization. I would be great if >> somebody >> > could tell me how this type of calculation can be set up. >> > >> > Regards, >> > Jens> >> > >> > >> >> >> -- >> J. Jules. From owner-chemistry@ccl.net Mon Dec 13 13:24:00 2010 From: "=?ISO-8859-1?Q?Ulf_Ekstr=F6m?= ulfek(!)few.vu.nl" To: CCL Subject: CCL: Queries on DFT functional Message-Id: <-43373-101213131148-31670-39vPaIrKn2gwGd/PMiIYvw^_^server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 13 Dec 2010 19:11:40 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Ulf_Ekstr=F6m?= [ulfek|*|few.vu.nl] On Mon, Dec 13, 2010 at 5:03 PM, Eli Lam elizabeth.shlam::gmail.com wrote: > > Sent to CCL by: "Eli  Lam" [elizabeth.shlam^-^gmail.com] > Thanks so much for your help! > > Actually I've run the TDDFT using PBE1PBE functional for a donor-acceptor molecule.  However, it seems > the lowest absorption band is much red shifted than the experimental one.  I've learnt that since HF may > blue shift the energy, I could add more portion of HF in the route for calculations. What do you want to get out of such a calculation? Of course you can get better "agreement" with experiment, but is that really telling you anything you don't know? The only time I would agree with adding more HF exchange is when your charge transfer excitation is mixing with low non-CT excitations in a way which makes the spectrum difficult to analyze. Otherwise you are just fitting your calculation to a known result. However, nowadays there are many functionals with good CT performance, i.e. CAM-B3LYP, LR-wPBE, M06-2x etc, so I don't think you should play with HF exchange just to reproduce knows numbers. Regards, Ulf Ekstrom From owner-chemistry@ccl.net Mon Dec 13 14:37:00 2010 From: "fatemeh moosavi fatemeh.moosavi##gmail.com" To: CCL Subject: CCL:G: Problem in Guassian freq calculation Message-Id: <-43374-101213063451-1085-qLsWPmA03E5mP1+jlbmL+g~!~server.ccl.net> X-Original-From: fatemeh moosavi Content-Type: multipart/alternative; boundary=0016e6d971090475b3049749172e Date: Mon, 13 Dec 2010 03:34:21 -0800 MIME-Version: 1.0 Sent to CCL by: fatemeh moosavi [fatemeh.moosavi]|[gmail.com] --0016e6d971090475b3049749172e Content-Type: text/plain; charset=ISO-8859-1 Dear Vijay Tak I think if you delete "cphf=noread", your job will run without error. On Sun, Dec 12, 2010 at 11:34 PM, Vijay Kumar Tak takvijay*|*gmail.com < owner-chemistry^ccl.net> wrote: > > Sent to CCL by: "Vijay Kumar Tak" [takvijay!=!gmail.com] > Hello, > There is a problem in calculating the frequency of an compund carrying a > three positive chages. I have optimized the conformation of trication which > consist of 88 atoms at B3LYP level. Then i am trying to calculate the > frequency of same conformation at the same level, but the out put file is > showing following error. > ****************************************** > Gaussian 09: IA32W-G09RevA.02 11-Jun-2009 > 11-Dec-2010 > ****************************************** > %nprocshared=8 > Will use up to 8 processors via shared memory. > %mem=1GB > %chk=E:\Guassian calculations\Trication\DFT-B3LYP\1Freq.chk > --------------------------------------------------------------- > # freq=noraman cphf=noread b3lyp/6-311+g(d,p) geom=connectivity > --------------------------------------------------------------- > 1/10=4,30=1,38=1,57=2/1,3; > 2/12=2,17=6,18=5,40=1/2; > 3/5=4,6=6,7=111,11=2,16=1,25=1,30=1,71=2,74=-5/1,2,3; > 4//1; > 5/5=2,38=5,98=1/2; > 8/6=4,10=90,11=11/1; > 11/6=1,8=1,9=11,15=111,16=1/1,2,10; > 10/6=1/2; > 6/7=2,8=2,9=2,10=2,18=1,28=1/1; > 7/8=1,10=1,25=1/1,2,3,16; > 1/10=4,30=1/3; > 99//99; > ----- > 1Freq > ----- > Symbolic Z-matrix: > Charge = 3 Multiplicity = 1 > C -14.05514 -0.30777 1.48727 > C -14.84798 0.78786 1.83187 > C -14.72668 1.98553 1.1309 > C -13.80815 2.09126 0.08739 > C -13.00564 0.99913 -0.25784 > C -13.13873 -0.20414 0.4453 > C -12.02369 1.11721 -1.39256 > N -10.61123 1.31574 -0.91687 > C -10.21931 2.04802 0.18506 > C -8.85798 2.0396 0.21013 > N -8.43244 1.29947 -0.87866 > C -9.51721 0.87568 -1.54268 > C -7.02846 1.03252 -1.25739 > C -6.31137 0.08478 -0.28811 > C -4.85723 -0.17144 -0.71843 > C -4.1112 -1.10244 0.25006 > C -2.66345 -1.3933 -0.18343 > C -1.98338 -2.34883 0.80213 > N -0.59636 -2.72048 0.42241 > C 0.49117 -2.54755 1.18283 > N 1.54931 -3.0916 0.57002 > C 1.11896 -3.63833 -0.62513 > C -0.21873 -3.40475 -0.71828 > C 2.90508 -3.24005 1.16662 > C 4.05788 -2.79091 0.26352 > C 4.15705 -1.27597 0.03719 > C 5.32799 -0.84492 -0.86707 > C 6.72808 -1.03907 -0.25782 > C 7.81353 -0.50618 -1.20285 > N 9.18436 -0.67399 -0.67628 > C 9.99921 0.31757 -0.28677 > N 11.16496 -0.20587 0.09609 > C 11.09966 -1.57792 -0.05343 > C 9.86287 -1.87229 -0.53766 > C 12.36011 0.5472 0.60983 > C 12.2046 2.03928 0.49535 > C 11.72322 2.78352 1.5785 > C 11.59043 4.167 1.47547 > C 11.93896 4.81416 0.29083 > C 12.42509 4.07915 -0.79052 > C 12.55974 2.69678 -0.68887 > H -14.16351 -1.24468 2.02048 > H -15.56841 0.70225 2.63662 > H -15.35334 2.83171 1.38566 > H -13.73327 3.01981 -0.46991 > H -12.54067 -1.06719 0.16897 > H -12.00763 0.21677 -2.00834 > H -12.26274 1.9685 -2.0319 > H -10.93532 2.49789 0.85127 > H -8.17029 2.4977 0.90001 > H -9.50739 0.28436 -2.44346 > H -7.04881 0.61717 -2.26637 > H -6.52158 1.99845 -1.3126 > H -6.32711 0.51258 0.71968 > H -6.8596 -0.86175 -0.23853 > H -4.8469 -0.60934 -1.72349 > H -4.32286 0.78307 -0.79029 > H -4.10859 -0.65585 1.2512 > H -4.65934 -2.04799 0.33501 > H -2.66532 -1.83432 -1.18567 > H -2.091 -0.46202 -0.2448 > H -1.92252 -1.90434 1.79676 > H -2.54458 -3.28181 0.8931 > H 0.50778 -2.06831 2.14791 > H 1.78181 -4.15552 -1.29704 > H -0.92084 -3.67961 -1.48655 > H 2.89481 -2.66901 2.09656 > H 3.01414 -4.29509 1.42588 > H 4.96385 -3.16166 0.75273 > H 4.00588 -3.31629 -0.69665 > H 4.23916 -0.76778 1.00571 > H 3.23041 -0.9144 -0.42205 > H 5.19336 0.21456 -1.10873 > H 5.26553 -1.38324 -1.82042 > H 6.91735 -2.09782 -0.05506 > H 6.79544 -0.51358 0.70079 > H 7.67679 0.56031 -1.38848 > H 7.77557 -1.01238 -2.17006 > H 9.76587 1.3689 -0.29299 > H 11.93069 -2.22061 0.18476 > H 9.4258 -2.81868 -0.80634 > H 13.21073 0.18858 0.02858 > H 12.49515 0.23879 1.64769 > H 11.477 2.28761 2.51228 > H 11.23562 4.73975 2.32397 > H 11.85051 5.89153 0.21621 > H 12.71813 4.58395 -1.70328 > H 12.96438 2.13382 -1.52421 > > > GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad > Berny optimization. > Initialization pass. > Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 > Number of steps in this run= 2 maximum allowed number of steps= 2. > GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad > > Stoichiometry C35H47N6(3+) > Framework group C1[X(C35H47N6)] > Deg. of freedom 258 > Full point group C1 NOp 1 > Largest Abelian subgroup C1 NOp 1 > Largest concise Abelian subgroup C1 NOp 1 > Standard orientation: > --------------------------------------------------------------------- > Center Atomic Atomic Coordinates (Angstroms) > Number Number Type X Y Z > --------------------------------------------------------------------- > 1 6 0 -14.055140 -0.307766 1.487270 > 2 6 0 -14.847981 0.787858 1.831866 > 3 6 0 -14.726677 1.985534 1.130895 > 4 6 0 -13.808148 2.091260 0.087392 > 5 6 0 -13.005645 0.999125 -0.257839 > 6 6 0 -13.138734 -0.204138 0.445304 > 7 6 0 -12.023692 1.117210 -1.392560 > 8 7 0 -10.611225 1.315743 -0.916872 > 9 6 0 -10.219311 2.048020 0.185057 > 10 6 0 -8.857979 2.039598 0.210133 > 11 7 0 -8.432440 1.299473 -0.878655 > 12 6 0 -9.517207 0.875681 -1.542684 > 13 6 0 -7.028455 1.032515 -1.257391 > 14 6 0 -6.311368 0.084778 -0.288110 > 15 6 0 -4.857232 -0.171438 -0.718427 > 16 6 0 -4.111197 -1.102435 0.250063 > 17 6 0 -2.663446 -1.393301 -0.183430 > 18 6 0 -1.983377 -2.348833 0.802131 > 19 7 0 -0.596363 -2.720478 0.422409 > 20 6 0 0.491172 -2.547550 1.182831 > 21 7 0 1.549314 -3.091600 0.570022 > 22 6 0 1.118956 -3.638332 -0.625134 > 23 6 0 -0.218727 -3.404747 -0.718276 > 24 6 0 2.905076 -3.240050 1.166616 > 25 6 0 4.057883 -2.790909 0.263519 > 26 6 0 4.157045 -1.275970 0.037194 > 27 6 0 5.327988 -0.844917 -0.867068 > 28 6 0 6.728078 -1.039068 -0.257817 > 29 6 0 7.813525 -0.506180 -1.202848 > 30 7 0 9.184359 -0.673991 -0.676284 > 31 6 0 9.999211 0.317569 -0.286767 > 32 7 0 11.164957 -0.205873 0.096087 > 33 6 0 11.099655 -1.577922 -0.053427 > 34 6 0 9.862871 -1.872290 -0.537662 > 35 6 0 12.360109 0.547195 0.609832 > 36 6 0 12.204601 2.039279 0.495350 > 37 6 0 11.723218 2.783523 1.578500 > 38 6 0 11.590427 4.166996 1.475465 > 39 6 0 11.938956 4.814158 0.290826 > 40 6 0 12.425085 4.079151 -0.790522 > 41 6 0 12.559738 2.696778 -0.688870 > 42 1 0 -14.163506 -1.244678 2.020477 > 43 1 0 -15.568414 0.702249 2.636615 > 44 1 0 -15.353339 2.831712 1.385663 > 45 1 0 -13.733274 3.019809 -0.469909 > 46 1 0 -12.540668 -1.067191 0.168965 > 47 1 0 -12.007630 0.216772 -2.008343 > 48 1 0 -12.262742 1.968498 -2.031902 > 49 1 0 -10.935324 2.497886 0.851274 > 50 1 0 -8.170292 2.497702 0.900012 > 51 1 0 -9.507394 0.284364 -2.443457 > 52 1 0 -7.048810 0.617168 -2.266372 > 53 1 0 -6.521579 1.998451 -1.312597 > 54 1 0 -6.327105 0.512579 0.719675 > 55 1 0 -6.859602 -0.861749 -0.238533 > 56 1 0 -4.846899 -0.609341 -1.723485 > 57 1 0 -4.322863 0.783067 -0.790291 > 58 1 0 -4.108592 -0.655852 1.251203 > 59 1 0 -4.659344 -2.047986 0.335008 > 60 1 0 -2.665316 -1.834321 -1.185671 > 61 1 0 -2.091002 -0.462021 -0.244797 > 62 1 0 -1.922516 -1.904336 1.796755 > 63 1 0 -2.544576 -3.281805 0.893097 > 64 1 0 0.507775 -2.068308 2.147908 > 65 1 0 1.781806 -4.155525 -1.297041 > 66 1 0 -0.920844 -3.679609 -1.486549 > 67 1 0 2.894807 -2.669013 2.096559 > 68 1 0 3.014140 -4.295093 1.425876 > 69 1 0 4.963853 -3.161656 0.752730 > 70 1 0 4.005879 -3.316291 -0.696652 > 71 1 0 4.239162 -0.767781 1.005710 > 72 1 0 3.230411 -0.914403 -0.422050 > 73 1 0 5.193359 0.214561 -1.108726 > 74 1 0 5.265526 -1.383240 -1.820424 > 75 1 0 6.917350 -2.097818 -0.055060 > 76 1 0 6.795441 -0.513577 0.700785 > 77 1 0 7.676786 0.560314 -1.388484 > 78 1 0 7.775572 -1.012384 -2.170056 > 79 1 0 9.765873 1.368902 -0.292993 > 80 1 0 11.930692 -2.220611 0.184757 > 81 1 0 9.425801 -2.818683 -0.806338 > 82 1 0 13.210734 0.188576 0.028579 > 83 1 0 12.495149 0.238787 1.647686 > 84 1 0 11.477000 2.287609 2.512282 > 85 1 0 11.235617 4.739753 2.323972 > 86 1 0 11.850508 5.891527 0.216208 > 87 1 0 12.718127 4.583952 -1.703277 > 88 1 0 12.964379 2.133818 -1.524213 > --------------------------------------------------------------------- > Rotational constants (GHZ): 0.1679224 0.0103802 0.0099533 > Standard basis: 6-311+G(d,p) (5D, 7F) > There are 1184 symmetry adapted basis functions of A symmetry. > Integral buffers will be 262144 words long. > Raffenetti 2 integral format. > Two-electron integral symmetry is turned on. > 1184 basis functions, 1852 primitive gaussians, 1225 cartesian basis > functions > 148 alpha electrons 148 beta electrons > nuclear repulsion energy 3740.7282424628 Hartrees. > NAtoms= 88 NActive= 88 NUniq= 88 SFac= 7.50D-01 NAtFMM= 80 > NAOKFM=T Big=T > One-electron integrals computed using PRISM. > NBasis= 1184 RedAO= T NBF= 1184 > NBsUse= 1184 1.00D-06 NBFU= 1184 > Harris functional with IExCor= 402 diagonalized for initial guess. > ExpMin= 4.38D-02 ExpMax= 6.29D+03 ExpMxC= 9.49D+02 IAcc=2 IRadAn= > 0 AccDes= 0.00D+00 > HarFok: IExCor= 402 AccDes= 0.00D+00 IRadAn= 0 IDoV= 1 > ScaDFX= 1.000000 1.000000 1.000000 1.000000 > FoFCou: FMM=F IPFlag= 0 FMFlag= 100000 FMFlg1= 2001 > NFxFlg= 0 DoJE=T BraDBF=F KetDBF=T FulRan=T > Omega= 0.000000 0.000000 1.000000 0.000000 0.000000 ICntrl= > 500 IOpCl= 0 > NMat0= 1 NMatS0= 1 NMatT0= 0 NMatD0= 1 NMtDS0= 0 > NMtDT0= 0 > I1Cent= 4 NGrid= 0. > Petite list used in FoFCou. > Initial guess orbital symmetries: > Occupied (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) > Virtual (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) > (A) (A) (A) (A) > The electronic state of the initial guess is 1-A. > Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. > Requested convergence on MAX density matrix=1.00D-06. > Requested convergence on energy=1.00D-06. > No special actions if energy rises. > Restarting incremental Fock formation. > SCF Done: E(RB3LYP) = -1690.21228532 A.U. after 28 cycles > Convg = 0.5107D-08 -V/T = 2.0046 > Range of M.O.s used for correlation: 1 1184 > NBasis= 1184 NAE= 148 NBE= 148 NFC= 0 NFV= 0 > NROrb= 1184 NOA= 148 NOB= 148 NVA= 1036 NVB= 1036 > > **** Warning!!: The largest alpha MO coefficient is 0.12683417D+03 > > PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. > PrsmSu: requested number of processors reduced to: 1 ShMem 1 Linda. > Symmetrizing basis deriv contribution to polar: > IMax=3 JMax=2 DiffMx= 0.00D+00 > G2DrvN: will do 4 centers at a time, making 23 passes doing > MaxLOS=2. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > Calling FoFCou, ICntrl= 3107 FMM=T I1Cent= 0 AccDes= 0.00D+00. > FoFDir/FoFCou used for L=0 through L=2. > End of G2Drv Frequency-dependent properties file 721 does not exist. > End of G2Drv Frequency-dependent properties file 722 does not exist. > IDoAtm=11111111111111111111111111111111111111111111111111 > IDoAtm=11111111111111111111111111111111111111 > Differentiating once with respect to electric field. > with respect to dipole field. > Differentiating once with respect to nuclear coordinates. > There are 267 degrees of freedom in the 1st order CPHF. > IDoFFX=5. > 267 vectors produced by pass 0 Test12= 1.53D-13 1.00D-09 XBig12= > 3.87D+02 6.76D+00. > AX will form 15 AO Fock derivatives at one time. > 267 vectors produced by pass 1 Test12= 1.53D-13 1.00D-09 XBig12= > 8.56D+01 1.11D+00. > 264 vectors produced by pass 2 Test12= 1.53D-13 1.00D-09 XBig12= > 5.91D-01 5.93D-02. > 264 vectors produced by pass 3 Test12= 1.53D-13 1.00D-09 XBig12= > 2.23D-03 3.14D-03. > 264 vectors produced by pass 4 Test12= 1.53D-13 1.00D-09 XBig12= > 4.09D-06 1.29D-04. > 264 vectors produced by pass 5 Test12= 1.53D-13 1.00D-09 XBig12= > 6.15D-09 4.16D-06. > 258 vectors produced by pass 6 Test12= 1.53D-13 1.00D-09 XBig12= > 1.40D-11 2.66D-07. > 236 vectors produced by pass 7 Test12= 1.53D-13 1.00D-09 XBig12= > 5.06D-13 2.87D-08. > 219 vectors produced by pass 8 Test12= 1.53D-13 1.00D-09 XBig12= > 2.56D-14 6.21D-09. > 199 vectors produced by pass 9 Test12= 1.53D-13 1.00D-09 XBig12= > 2.12D-14 5.20D-09. > 177 vectors produced by pass 10 Test12= 1.53D-13 1.00D-09 XBig12= > 2.01D-14 5.01D-09. > Internal consistency error detected in FileIO for unit 1 I= 7 J= 0 > IFail= 1. > > > dumping /fiocom/, unit = 1 NFiles = 88 SizExt = 32768 WInBlk = > 512 > defal = F LstWrd = -1962280960 FType=2 FMxFil=10000 > > Number 0 0 0 0 0 0 > 0 501 > Base 11258363 10315776 73707520 18034688 11021824 > 362994176-1962321632 23552 > End 11720192 10317312 92399104 22244864 11023360 > 772379936-1962280960 24552 > End1 11720192 10317312 92399104 22244864 11023360 > 772379936-1962280960 24576 > Wr Pntr 11258363 10315776 73707520 18034688 11021824 362994176 > 1757205680 23552 > Rd Pntr 11258363 10315776 73707520 18034688 11021824 362994176 > 1757205680 23552 > Length 461829 1536 18691584 4210176 1536 409385760 > 40672 1000 > > Number 502 503 507 508 511 514 > 515 516 > Base 275968 96256 97280 284160 225280 5214208 > 2407936 303104 > End 279797 96829 98033 284175 260526 5915728 > 5214016 2407664 > End1 280064 97280 98304 284672 260608 5916160 > 5214208 2407936 > Wr Pntr 275968 96256 97280 284160 225280 5214208 > 2407936 303104 > Rd Pntr 275968 96256 97280 284160 225280 5214208 > 2407936 303104 > Length 3829 573 753 15 35246 701520 > 2806080 2104560 > > Number 517 518 520 521 522 523 > 524 526 > Base 10208768 8103936 301568 268800 11019264 10313216 > 11720192 14526976 > End 10312960 10208496 301573 268835 11021632 10315584 > 13122048 15928832 > End1 10313216 10208768 302080 269312 11021824 10315776 > 13122048 15928832 > Wr Pntr 10208768 8103936 301568 268800 11019264 10313216 > 11720192 14526976 > Rd Pntr 10208768 8103936 301568 268800 11019264 10313216 > 11720192 14526976 > Length 104192 2104560 5 35 2368 2368 > 1401856 1401856 > > Number 528 530 532 534 536 538 > 545 547 > Base 13122048 10317312 13825024 15928832 16630784 17332736 > 11025408 11026944 > End 13823568 11018832 14526544 16630352 17332304 18034256 > 11025422 11029312 > End1 13824000 11019264 14526976 16630784 17332736 18034688 > 11025920 11029504 > Wr Pntr 13122048 10317312 13825024 15928832 16630784 17332736 > 11025408 11026944 > Rd Pntr 13122048 10317312 13825024 15928832 16630784 17332736 > 11025408 11026944 > Length 701520 701520 701520 701520 701520 701520 > 14 2368 > > Number 548 551 552 559 562 563 > 565 569 > Base 22946816 267264 22016 43008 260608 13824000 > 283648 11024896 > End 24348672 267289 22032 43009 266545 13824592 > 283865 11024897 > End1 24348672 267776 22528 43520 266752 13825024 > 284160 11025408 > Wr Pntr 22946816 267264 22016 43008 260608 13824000 > 283648 11024896 > Rd Pntr 22946816 267264 22016 43008 260608 13824000 > 283648 11024896 > Length 1401856 25 16 1 5937 592 > 217 1 > > Number 571 575 577 579 580 581 > 582 583 > Base 22244864 100864 282112 266752 41472 282624 > 280064 43520 > End 22946384 225207 282138 266796 42677 283248 > 281840 43565 > End1 22946816 225280 282624 267264 43008 283648 > 282112 44032 > Wr Pntr 22244864 100864 282112 266752 41472 282624 > 280064 43520 > Rd Pntr 22244864 100864 282112 266752 41472 282624 > 280064 43520 > Length 701520 124343 26 44 1205 624 > 1776 45 > > Number 584 588 590 598 600 603 > 605 606 > Base 284672 24348672 93810176 44032 11103744 302080 > 302592 11023360 > End 285200 26453232 281116016 44034 11104647 302081 > 302593 11024544 > End1 285696 26453504 281116160 44544 11104768 302592 > 303104 11024896 > Wr Pntr 284672 24348672 93810176 44032 11103744 302080 > 302592 11023360 > Rd Pntr 284672 24348672 93810176 44032 11103744 302080 > 302592 11023360 > Length 528 2104560 187305840 2 903 1 > 1 1184 > > Number 607 619 634 670 674 685 > 694 695 > Base 11025920 285696 92399104 269312 98304 5916160 > 11029504 298496 > End 11026512 298421 93809785 275761 98936 7318016 > 11031872 301252 > End1 11026944 298496 93810176 275968 99328 7318016 > 11032064 301568 > Wr Pntr 11025920 285696 92399104 269312 98304 5916160 > 11029504 298496 > Rd Pntr 11025920 285696 92399104 269312 98304 5916160 > 11029504 298496 > Length 592 12725 1410681 6449 632 1401856 > 2368 2756 > > Number 698 742 989 991 992 993 > 994 995 > Base 267776 7318016 24576 37888 37376 23040 > 20480 22528 > End 268304 8103928 37076 41169 37381 23140 > 20510 22538 > End1 268800 8103936 37376 41472 37888 23552 > 20992 23040 > Wr Pntr 267776 7318016 24576 37888 37376 23040 > 20480 22528 > Rd Pntr 267776 7318016 24576 37888 37376 23040 > 20480 22528 > Length 528 785912 12500 3281 5 100 > 30 10 > > Number 996 997 998 999 2999 3001 > 3003 3005 > Base 21504 99328 20992 44544 11032064 28558848 > 281116160 69497856 > End 21604 100571 21192 95796 11103353 69497424 > 322054736 71602416 > End1 22016 100864 21504 96256 11103744 69497856 > 322055168 71602688 > Wr Pntr 21504 99328 20992 44544 11032064 28558848 > 281116160 69497856 > Rd Pntr 21504 99328 20992 44544 11032064 28558848 > 281116160 69497856 > Length 100 1243 200 51252 71289 40938576 > 40938576 2104560 > > Number 3007 3026 9994 9995 9996 9997 > 9998 9999 > Base 71602688 27856896 1181765696 772379936 1757205680 11104768 > 322055168 26453504 > End 73707248 28558416 1757205680 1181765696-1962321632 11258363 > 362993744 27856544 > End1 73707520 28558848 1757205680 1181765696-1962321632 11258363 > 362994176 27856896 > Wr Pntr 71602688 27856896 1181765696 772379936 1757205680 11104768 > 322055168 26453504 > Rd Pntr 71602688 27856896 1181765696 772379936 1757205680 11104768 > 322055168 26453504 > Length 2104560 701520 575439984 409385760 575439984 153595 > 40938576 1403040 > > > dumping /fiocom/, unit = 2 NFiles = 7 SizExt = 0 WInBlk = > 512 > defal = F LstWrd = 2838528 FType=2 FMxFil=10000 > > Number 0 508 522 536 538 634 > 998 > Base 2836784 20480 20695 1433744 2135264 23063 > 20495 > End 2838528 20495 23063 2135264 2836784 1433744 > 20695 > End1 2838528 20495 23063 2135264 2836784 1433744 > 20695 > Wr Pntr 2836784 20480 20695 1433744 2135264 23063 > 20495 > Rd Pntr 2836784 20480 20695 1433744 2135264 23063 > 20495 > Length 1744 15 2368 701520 701520 1410681 > 200 > > > dumping /fiocom/, unit = 3 NFiles = 1 SizExt = 524288 WInBlk = > 512 > defal = T LstWrd = 67072 FType=2 FMxFil=10000 > > Number 0 > Base 20480 > End 67072 > End1 67072 > Wr Pntr 20480 > Rd Pntr 20480 > Length 46592 > Error termination in NtrErr: > NtrErr called from FIOCnC. > > Can anybody tell me that what is the problem in my calculation and why it > is coming and what is its solution? Thank you very much in advance. > With regards, > Vijay Tak> > > --0016e6d971090475b3049749172e Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Vijay Tak
I think if you delete "cphf=3Dnoread", your job will run wit= hout error.
On Sun, Dec 12, 2010 at 11:34 PM, Vijay Kumar Ta= k takvijay*|*gmail.com &= lt;owner-chemistry^ccl.net&g= t; wrote:

Sent to CCL by: "Vijay = Kumar Tak" [takvijay!=3D!gmail.com]
Hello,
There is a problem in calculating the frequency of an compund car= rying a three positive chages. I have optimized the conformation of tricati= on which consist of 88 atoms at B3LYP level. Then =A0i am trying to calcula= te the frequency of same conformation at the same level, but the out =A0put= file is showing following error.
=A0******************************************
=A0Gaussian 09: =A0IA32W-G= 09RevA.02 11-Jun-2009
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A011-Dec-2010
=A0*= *****************************************
=A0%nprocshared=3D8
=A0Will= use up to =A0 =A08 processors via shared memory.
=A0%mem=3D1GB
=A0%chk=3DE:\Guassian calculations\Trication\DFT-B3LYP\1Fr= eq.chk
=A0--------------------------------------------------------------= -
=A0# freq=3Dnoraman cphf=3Dnoread b3lyp/6-311+g(d,p) geom=3Dconnectivi= ty
=A0--------------------------------------------------------------- =A01/10=3D4,30=3D1,38=3D1,57=3D2/1,3;
=A02/12=3D2,17=3D6,18=3D5,40=3D1/2= ;
=A03/5=3D4,6=3D6,7=3D111,11=3D2,16=3D1,25=3D1,30=3D1,71=3D2,74=3D-5/1,= 2,3;
=A04//1;
=A05/5=3D2,38=3D5,98=3D1/2;
=A08/6=3D4,10=3D90,11=3D= 11/1;
=A011/6=3D1,8=3D1,9=3D11,15=3D111,16=3D1/1,2,10;
=A010/6=3D1/2;=
=A06/7=3D2,8=3D2,9=3D2,10=3D2,18=3D1,28=3D1/1;
=A07/8=3D1,10=3D1,25=3D1/= 1,2,3,16;
=A01/10=3D4,30=3D1/3;
=A099//99;
=A0-----
=A01Freq=A0-----
=A0Symbolic Z-matrix:
=A0Charge =3D =A03 Multiplicity =3D 1=
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-14.05514 =A0-0.30777 =A0 1= .48727
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-14.84798 =A0 0.78786 =A0 1.831= 87
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-14.72668 =A0 1.98553 =A0= 1.1309
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-13.80815 =A0 2.0912= 6 =A0 0.08739
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-13.00564 =A0 = 0.99913 =A0-0.25784
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-13.1387= 3 =A0-0.20414 =A0 0.4453
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-12.02369 =A0 1.11721 =A0-1.392= 56
=A0N =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-10.61123 =A0 1.31574 =A0= -0.91687
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-10.21931 =A0 2.048= 02 =A0 0.18506
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-8.85798 =A0 = 2.0396 =A0 =A00.21013
=A0N =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-8.432= 44 =A0 1.29947 =A0-0.87866
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-9.51721 =A0 0.87568 =A0-1.5426= 8
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-7.02846 =A0 1.03252 =A0-1= .25739
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-6.31137 =A0 0.08478 = =A0-0.28811
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-4.85723 =A0-0.1= 7144 =A0-0.71843
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-4.1112 =A0= -1.10244 =A0 0.25006
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-2.66345 =A0-1.3933 =A0 -0.1834= 3
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-1.98338 =A0-2.34883 =A0 0= .80213
=A0N =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-0.59636 =A0-2.72048 = =A0 0.42241
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 0.49117 =A0-2.5= 4755 =A0 1.18283
=A0N =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1.54931 = =A0-3.0916 =A0 =A00.57002
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1.11896 =A0-3.63833 =A0-0.6251= 3
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-0.21873 =A0-3.40475 =A0-0= .71828
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 2.90508 =A0-3.24005 = =A0 1.16662
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 4.05788 =A0-2.7= 9091 =A0 0.26352
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 4.15705 = =A0-1.27597 =A0 0.03719
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 5.32799 =A0-0.84492 =A0-0.8670= 7
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 6.72808 =A0-1.03907 =A0-0= .25782
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 7.81353 =A0-0.50618 = =A0-1.20285
=A0N =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 9.18436 =A0-0.6= 7399 =A0-0.67628
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 9.99921 = =A0 0.31757 =A0-0.28677
=A0N =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 11.16496 =A0-0.20587 =A0 0.096= 09
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 11.09966 =A0-1.57792 =A0= -0.05343
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 9.86287 =A0-1.8722= 9 =A0-0.53766
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 12.36011 =A0 = 0.5472 =A0 =A00.60983
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 12.20= 46 =A0 2.03928 =A0 0.49535
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 11.72322 =A0 2.78352 =A0 1.578= 5
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 11.59043 =A0 4.167 =A0 = =A0 1.47547
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 11.93896 =A0 4.= 81416 =A0 0.29083
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 12.42509 = =A0 4.07915 =A0-0.79052
=A0C =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 12.= 55974 =A0 2.69678 =A0-0.68887
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-14.16351 =A0-1.24468 =A0 2.020= 48
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-15.56841 =A0 0.70225 =A0= 2.63662
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-15.35334 =A0 2.831= 71 =A0 1.38566
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-13.73327 =A0= 3.01981 =A0-0.46991
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-12.54067 =A0-1.06719 =A0 0.168= 97
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-12.00763 =A0 0.21677 =A0-2.008= 34
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-12.26274 =A0 1.9685 =A0 = -2.0319
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-10.93532 =A0 2.4978= 9 =A0 0.85127
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-8.17029 =A0 2= .4977 =A0 =A00.90001
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-9.5073= 9 =A0 0.28436 =A0-2.44346
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-7.04881 =A0 0.61717 =A0-2.2663= 7
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-6.52158 =A0 1.99845 =A0-1= .3126
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-6.32711 =A0 0.51258 = =A0 0.71968
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-6.8596 =A0 -0.8= 6175 =A0-0.23853
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-4.8469 =A0= -0.60934 =A0-1.72349
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-4.32286 =A0 0.78307 =A0-0.7902= 9
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-4.10859 =A0-0.65585 =A0 1= .2512
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-4.65934 =A0-2.04799 = =A0 0.33501
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-2.66532 =A0-1.8= 3432 =A0-1.18567
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-2.091 =A0 = =A0-0.46202 =A0-0.2448
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-1.92252 =A0-1.90434 =A0 1.7967= 6
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-2.54458 =A0-3.28181 =A0 0= .8931
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 0.50778 =A0-2.06831 = =A0 2.14791
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1.78181 =A0-4.1= 5552 =A0-1.29704
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0-0.92084 = =A0-3.67961 =A0-1.48655
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 2.89481 =A0-2.66901 =A0 2.0965= 6
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 3.01414 =A0-4.29509 =A0 1= .42588
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 4.96385 =A0-3.16166 = =A0 0.75273
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 4.00588 =A0-3.3= 1629 =A0-0.69665
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 4.23916 = =A0-0.76778 =A0 1.00571
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 3.23041 =A0-0.9144 =A0 -0.4220= 5
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 5.19336 =A0 0.21456 =A0-1= .10873
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 5.26553 =A0-1.38324 = =A0-1.82042
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 6.91735 =A0-2.0= 9782 =A0-0.05506
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 6.79544 = =A0-0.51358 =A0 0.70079
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 7.67679 =A0 0.56031 =A0-1.3884= 8
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 7.77557 =A0-1.01238 =A0-2= .17006
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 9.76587 =A0 1.3689 = =A0 -0.29299
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 11.93069 =A0-2= .22061 =A0 0.18476
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 9.4258 = =A0 -2.81868 =A0-0.80634
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 13.21073 =A0 0.18858 =A0 0.028= 58
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 12.49515 =A0 0.23879 =A0= 1.64769
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 11.477 =A0 =A02.28= 761 =A0 2.51228
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 11.23562 = =A0 4.73975 =A0 2.32397
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 11.= 85051 =A0 5.89153 =A0 0.21621
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 12.71813 =A0 4.58395 =A0-1.703= 28
=A0H =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 12.96438 =A0 2.13382 =A0= -1.52421


=A0GradGradGradGradGradGradGradGradGradGradGradGradGrad= GradGradGradGradGrad
=A0Berny optimization.
=A0Initialization pass. =A0Trust Radius=3D3.00D-01 FncErr=3D1.00D-07 GrdErr=3D1.00D-07
=A0Number= of steps in this run=3D =A0 2 maximum allowed number of steps=3D =A0 2.=A0GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGra= d

=A0Stoichiometry =A0 =A0C35H47N6(3+)
=A0Framework group =A0C1[X(C35H47N6)]
=A0Deg. of freedom =A0 258
=A0F= ull point group =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 C1 =A0 =A0 =A0NOp =A0 1
= =A0Largest Abelian subgroup =A0 =A0 =A0 =A0 C1 =A0 =A0 =A0NOp =A0 1
=A0L= argest concise Abelian subgroup C1 =A0 =A0 =A0NOp =A0 1
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 Standard orientation:
= =A0---------------------------------------------------------------------=A0Center =A0 =A0 Atomic =A0 =A0 =A0Atomic =A0 =A0 =A0 =A0 =A0 =A0 Coordin= ates (Angstroms)
=A0Number =A0 =A0 Number =A0 =A0 =A0 Type =A0 =A0 =A0 = =A0 =A0 =A0 X =A0 =A0 =A0 =A0 =A0 Y =A0 =A0 =A0 =A0 =A0 Z
=A0---------------------------------------------------------------------=A0 =A0 =A01 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-14.055= 140 =A0 -0.307766 =A0 =A01.487270
=A0 =A0 =A02 =A0 =A0 =A0 =A0 =A06 =A0 = =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-14.847981 =A0 =A00.787858 =A0 =A01.831866
=A0 =A0 =A03 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-14.7266= 77 =A0 =A01.985534 =A0 =A01.130895
=A0 =A0 =A04 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-13.8081= 48 =A0 =A02.091260 =A0 =A00.087392
=A0 =A0 =A05 =A0 =A0 =A0 =A0 =A06 =A0= =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-13.005645 =A0 =A00.999125 =A0 -0.257839
= =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-13.1387= 34 =A0 -0.204138 =A0 =A00.445304
=A0 =A0 =A07 =A0 =A0 =A0 =A0 =A06 =A0 = =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-12.023692 =A0 =A01.117210 =A0 -1.392560
=A0 =A0 =A08 =A0 =A0 =A0 =A0 =A07 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-10.6112= 25 =A0 =A01.315743 =A0 -0.916872
=A0 =A0 =A09 =A0 =A0 =A0 =A0 =A06 =A0 = =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-10.219311 =A0 =A02.048020 =A0 =A00.185057
= =A0 =A0 10 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -8.857979= =A0 =A02.039598 =A0 =A00.210133
=A0 =A0 11 =A0 =A0 =A0 =A0 =A07 =A0 =A0= =A0 =A0 =A0 0 =A0 =A0 =A0 -8.432440 =A0 =A01.299473 =A0 -0.878655
=A0 =A0 12 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -9.517207= =A0 =A00.875681 =A0 -1.542684
=A0 =A0 13 =A0 =A0 =A0 =A0 =A06 =A0 =A0 = =A0 =A0 =A0 0 =A0 =A0 =A0 -7.028455 =A0 =A01.032515 =A0 -1.257391
=A0 = =A0 14 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -6.311368 =A0= =A00.084778 =A0 -0.288110
=A0 =A0 15 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 = =A0 =A0 0 =A0 =A0 =A0 -4.857232 =A0 -0.171438 =A0 -0.718427
=A0 =A0 16 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -4.111197= =A0 -1.102435 =A0 =A00.250063
=A0 =A0 17 =A0 =A0 =A0 =A0 =A06 =A0 =A0 = =A0 =A0 =A0 0 =A0 =A0 =A0 -2.663446 =A0 -1.393301 =A0 -0.183430
=A0 =A0 = 18 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -1.983377 =A0 -2.= 348833 =A0 =A00.802131
=A0 =A0 19 =A0 =A0 =A0 =A0 =A07 =A0 =A0 =A0 =A0 = =A0 0 =A0 =A0 =A0 -0.596363 =A0 -2.720478 =A0 =A00.422409
=A0 =A0 20 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A00.4911= 72 =A0 -2.547550 =A0 =A01.182831
=A0 =A0 21 =A0 =A0 =A0 =A0 =A07 =A0 =A0= =A0 =A0 =A0 0 =A0 =A0 =A0 =A01.549314 =A0 -3.091600 =A0 =A00.570022
=A0= =A0 22 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A01.118956 = =A0 -3.638332 =A0 -0.625134
=A0 =A0 23 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 = =A0 =A0 0 =A0 =A0 =A0 -0.218727 =A0 -3.404747 =A0 -0.718276
=A0 =A0 24 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A02.9050= 76 =A0 -3.240050 =A0 =A01.166616
=A0 =A0 25 =A0 =A0 =A0 =A0 =A06 =A0 =A0= =A0 =A0 =A0 0 =A0 =A0 =A0 =A04.057883 =A0 -2.790909 =A0 =A00.263519
=A0= =A0 26 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A04.157045 = =A0 -1.275970 =A0 =A00.037194
=A0 =A0 27 =A0 =A0 =A0 =A0 =A06 =A0 =A0 = =A0 =A0 =A0 0 =A0 =A0 =A0 =A05.327988 =A0 -0.844917 =A0 -0.867068
=A0 =A0 28 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A06.7280= 78 =A0 -1.039068 =A0 -0.257817
=A0 =A0 29 =A0 =A0 =A0 =A0 =A06 =A0 =A0 = =A0 =A0 =A0 0 =A0 =A0 =A0 =A07.813525 =A0 -0.506180 =A0 -1.202848
=A0 = =A0 30 =A0 =A0 =A0 =A0 =A07 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A09.184359 = =A0 -0.673991 =A0 -0.676284
=A0 =A0 31 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 = =A0 =A0 0 =A0 =A0 =A0 =A09.999211 =A0 =A00.317569 =A0 -0.286767
=A0 =A0 32 =A0 =A0 =A0 =A0 =A07 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 11.164957= =A0 -0.205873 =A0 =A00.096087
=A0 =A0 33 =A0 =A0 =A0 =A0 =A06 =A0 =A0 = =A0 =A0 =A0 0 =A0 =A0 =A0 11.099655 =A0 -1.577922 =A0 -0.053427
=A0 =A0 = 34 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A09.862871 =A0 -= 1.872290 =A0 -0.537662
=A0 =A0 35 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 = =A0 0 =A0 =A0 =A0 12.360109 =A0 =A00.547195 =A0 =A00.609832
=A0 =A0 36 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 12.204601= =A0 =A02.039279 =A0 =A00.495350
=A0 =A0 37 =A0 =A0 =A0 =A0 =A06 =A0 =A0= =A0 =A0 =A0 0 =A0 =A0 =A0 11.723218 =A0 =A02.783523 =A0 =A01.578500
=A0= =A0 38 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 11.590427 = =A0 =A04.166996 =A0 =A01.475465
=A0 =A0 39 =A0 =A0 =A0 =A0 =A06 =A0 =A0 = =A0 =A0 =A0 0 =A0 =A0 =A0 11.938956 =A0 =A04.814158 =A0 =A00.290826
=A0 =A0 40 =A0 =A0 =A0 =A0 =A06 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 12.425085= =A0 =A04.079151 =A0 -0.790522
=A0 =A0 41 =A0 =A0 =A0 =A0 =A06 =A0 =A0 = =A0 =A0 =A0 0 =A0 =A0 =A0 12.559738 =A0 =A02.696778 =A0 -0.688870
=A0 = =A0 42 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-14.163506 =A0= -1.244678 =A0 =A02.020477
=A0 =A0 43 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 = =A0 =A0 0 =A0 =A0 =A0-15.568414 =A0 =A00.702249 =A0 =A02.636615
=A0 =A0 44 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-15.353339= =A0 =A02.831712 =A0 =A01.385663
=A0 =A0 45 =A0 =A0 =A0 =A0 =A01 =A0 =A0= =A0 =A0 =A0 0 =A0 =A0 =A0-13.733274 =A0 =A03.019809 =A0 -0.469909
=A0 = =A0 46 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-12.540668 =A0= -1.067191 =A0 =A00.168965
=A0 =A0 47 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 = =A0 =A0 0 =A0 =A0 =A0-12.007630 =A0 =A00.216772 =A0 -2.008343
=A0 =A0 48 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0-12.262742= =A0 =A01.968498 =A0 -2.031902
=A0 =A0 49 =A0 =A0 =A0 =A0 =A01 =A0 =A0 = =A0 =A0 =A0 0 =A0 =A0 =A0-10.935324 =A0 =A02.497886 =A0 =A00.851274
=A0 = =A0 50 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -8.170292 =A0= =A02.497702 =A0 =A00.900012
=A0 =A0 51 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0= =A0 =A0 0 =A0 =A0 =A0 -9.507394 =A0 =A00.284364 =A0 -2.443457
=A0 =A0 52 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -7.048810= =A0 =A00.617168 =A0 -2.266372
=A0 =A0 53 =A0 =A0 =A0 =A0 =A01 =A0 =A0 = =A0 =A0 =A0 0 =A0 =A0 =A0 -6.521579 =A0 =A01.998451 =A0 -1.312597
=A0 = =A0 54 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -6.327105 =A0= =A00.512579 =A0 =A00.719675
=A0 =A0 55 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0= =A0 =A0 0 =A0 =A0 =A0 -6.859602 =A0 -0.861749 =A0 -0.238533
=A0 =A0 56 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -4.846899= =A0 -0.609341 =A0 -1.723485
=A0 =A0 57 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0= =A0 =A0 0 =A0 =A0 =A0 -4.322863 =A0 =A00.783067 =A0 -0.790291
=A0 =A0 5= 8 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -4.108592 =A0 -0.6= 55852 =A0 =A01.251203
=A0 =A0 59 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 = =A0 0 =A0 =A0 =A0 -4.659344 =A0 -2.047986 =A0 =A00.335008
=A0 =A0 60 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -2.665316= =A0 -1.834321 =A0 -1.185671
=A0 =A0 61 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0= =A0 =A0 0 =A0 =A0 =A0 -2.091002 =A0 -0.462021 =A0 -0.244797
=A0 =A0 62 = =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -1.922516 =A0 -1.904= 336 =A0 =A01.796755
=A0 =A0 63 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 = 0 =A0 =A0 =A0 -2.544576 =A0 -3.281805 =A0 =A00.893097
=A0 =A0 64 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A00.5077= 75 =A0 -2.068308 =A0 =A02.147908
=A0 =A0 65 =A0 =A0 =A0 =A0 =A01 =A0 =A0= =A0 =A0 =A0 0 =A0 =A0 =A0 =A01.781806 =A0 -4.155525 =A0 -1.297041
=A0 = =A0 66 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 -0.920844 =A0= -3.679609 =A0 -1.486549
=A0 =A0 67 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0= =A0 0 =A0 =A0 =A0 =A02.894807 =A0 -2.669013 =A0 =A02.096559
=A0 =A0 68 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A03.0141= 40 =A0 -4.295093 =A0 =A01.425876
=A0 =A0 69 =A0 =A0 =A0 =A0 =A01 =A0 =A0= =A0 =A0 =A0 0 =A0 =A0 =A0 =A04.963853 =A0 -3.161656 =A0 =A00.752730
=A0= =A0 70 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A04.005879 = =A0 -3.316291 =A0 -0.696652
=A0 =A0 71 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 = =A0 =A0 0 =A0 =A0 =A0 =A04.239162 =A0 -0.767781 =A0 =A01.005710
=A0 =A0 72 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A03.2304= 11 =A0 -0.914403 =A0 -0.422050
=A0 =A0 73 =A0 =A0 =A0 =A0 =A01 =A0 =A0 = =A0 =A0 =A0 0 =A0 =A0 =A0 =A05.193359 =A0 =A00.214561 =A0 -1.108726
=A0 = =A0 74 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A05.265526 = =A0 -1.383240 =A0 -1.820424
=A0 =A0 75 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 = =A0 =A0 0 =A0 =A0 =A0 =A06.917350 =A0 -2.097818 =A0 -0.055060
=A0 =A0 76 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A06.7954= 41 =A0 -0.513577 =A0 =A00.700785
=A0 =A0 77 =A0 =A0 =A0 =A0 =A01 =A0 =A0= =A0 =A0 =A0 0 =A0 =A0 =A0 =A07.676786 =A0 =A00.560314 =A0 -1.388484
=A0= =A0 78 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A07.775572 = =A0 -1.012384 =A0 -2.170056
=A0 =A0 79 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 = =A0 =A0 0 =A0 =A0 =A0 =A09.765873 =A0 =A01.368902 =A0 -0.292993
=A0 =A0 80 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 11.930692= =A0 -2.220611 =A0 =A00.184757
=A0 =A0 81 =A0 =A0 =A0 =A0 =A01 =A0 =A0 = =A0 =A0 =A0 0 =A0 =A0 =A0 =A09.425801 =A0 -2.818683 =A0 -0.806338
=A0 = =A0 82 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 13.210734 =A0= =A00.188576 =A0 =A00.028579
=A0 =A0 83 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0= =A0 =A0 0 =A0 =A0 =A0 12.495149 =A0 =A00.238787 =A0 =A01.647686
=A0 =A0 84 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 11.477000= =A0 =A02.287609 =A0 =A02.512282
=A0 =A0 85 =A0 =A0 =A0 =A0 =A01 =A0 =A0= =A0 =A0 =A0 0 =A0 =A0 =A0 11.235617 =A0 =A04.739753 =A0 =A02.323972
=A0= =A0 86 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 11.850508 = =A0 =A05.891527 =A0 =A00.216208
=A0 =A0 87 =A0 =A0 =A0 =A0 =A01 =A0 =A0 = =A0 =A0 =A0 0 =A0 =A0 =A0 12.718127 =A0 =A04.583952 =A0 -1.703277
=A0 =A0 88 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 12.964379= =A0 =A02.133818 =A0 -1.524213
=A0--------------------------------------= -------------------------------
=A0Rotational constants (GHZ): =A0 =A0 = =A00.1679224 =A0 =A0 =A00.0103802 =A0 =A0 =A00.0099533
=A0Standard basis: 6-311+G(d,p) (5D, 7F)
=A0There are =A01184 symmetry a= dapted basis functions of A =A0 symmetry.
=A0Integral buffers will be = =A0 =A0262144 words long.
=A0Raffenetti 2 integral format.
=A0Two-ele= ctron integral symmetry is turned on.
=A01184 basis functions, =A01852 primitive gaussians, =A01225 cartesian bas= is functions
=A0 148 alpha electrons =A0 =A0 =A0148 beta electrons
= =A0 =A0 =A0 nuclear repulsion energy =A0 =A0 =A03740.7282424628 Hartrees.=A0NAtoms=3D =A0 88 NActive=3D =A0 88 NUniq=3D =A0 88 SFac=3D 7.50D-01 NA= tFMM=3D =A0 80 NAOKFM=3DT Big=3DT
=A0One-electron integrals computed using PRISM.
=A0NBasis=3D =A01184 Red= AO=3D T =A0NBF=3D =A01184
=A0NBsUse=3D =A01184 1.00D-06 NBFU=3D =A01184<= br>=A0Harris functional with IExCor=3D =A0402 diagonalized for initial gues= s.
=A0ExpMin=3D 4.38D-02 ExpMax=3D 6.29D+03 ExpMxC=3D 9.49D+02 IAcc=3D2 = IRadAn=3D =A0 =A0 =A0 =A0 0 AccDes=3D 0.00D+00
=A0HarFok: =A0IExCor=3D =A0402 AccDes=3D 0.00D+00 IRadAn=3D =A0 =A0 =A0 =A0= 0 IDoV=3D 1
=A0ScaDFX=3D =A01.000000 =A01.000000 =A01.000000 =A01.00000= 0
=A0FoFCou: FMM=3DF IPFlag=3D =A0 =A0 =A0 =A0 =A0 0 FMFlag=3D =A0 =A0 = =A0100000 FMFlg1=3D =A0 =A0 =A0 =A02001
=A0 =A0 =A0 =A0 NFxFlg=3D =A0 = =A0 =A0 =A0 =A0 0 DoJE=3DT BraDBF=3DF KetDBF=3DT FulRan=3DT
=A0 =A0 =A0 =A0 Omega=3D =A00.000000 =A00.000000 =A01.000000 =A00.000000 = =A00.000000 ICntrl=3D =A0 =A0 500 IOpCl=3D =A00
=A0 =A0 =A0 =A0 NMat0=3D= =A0 =A01 NMatS0=3D =A0 =A01 NMatT0=3D =A0 =A00 NMatD0=3D =A0 =A01 NMtDS0= =3D =A0 =A00 NMtDT0=3D =A0 =A00
=A0 =A0 =A0 =A0 I1Cent=3D =A0 =A0 =A0 = =A0 =A0 4 NGrid=3D =A0 =A0 =A0 =A0 =A0 0.
=A0Petite list used in FoFCou.
=A0Initial guess orbital symmetries:
= =A0 =A0 =A0 Occupied =A0(A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A)
=A0 =A0 =A0 Virt= ual =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A) (A)= (A) (A) (A) (A) (A) (A) (A)
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 (A) (A) (A) (A)
=A0The electronic state = of the initial guess is 1-A.
=A0Requested convergence on RMS density mat= rix=3D1.00D-08 within 128 cycles.
=A0Requested convergence on MAX densit= y matrix=3D1.00D-06.
=A0Requested convergence on =A0 =A0 =A0 =A0 =A0 =A0 energy=3D1.00D-06.
= =A0No special actions if energy rises.
=A0Restarting incremental Fock fo= rmation.
=A0SCF Done: =A0E(RB3LYP) =3D =A0-1690.21228532 =A0 =A0 A.U. af= ter =A0 28 cycles
=A0 =A0 =A0 =A0 =A0 =A0 Convg =A0=3D =A0 =A00.5107D-08= =A0 =A0 =A0 =A0 =A0 =A0 -V/T =3D =A02.0046
=A0Range of M.O.s used for correlation: =A0 =A0 1 =A01184
=A0NBasis=3D = =A01184 NAE=3D =A0 148 NBE=3D =A0 148 NFC=3D =A0 =A0 0 NFV=3D =A0 =A0 0
= =A0NROrb=3D =A0 1184 NOA=3D =A0 148 NOB=3D =A0 148 NVA=3D =A01036 NVB=3D = =A01036

=A0**** Warning!!: The largest alpha MO coefficient is =A00.= 12683417D+03

=A0PrsmSu: =A0requested number of processors reduced to: =A0 1 ShMem = =A0 1 Linda.
=A0PrsmSu: =A0requested number of processors reduced to: = =A0 1 ShMem =A0 1 Linda.
=A0Symmetrizing basis deriv contribution to pol= ar:
=A0IMax=3D3 JMax=3D2 DiffMx=3D 0.00D+00
=A0G2DrvN: will do =A0 =A0 4 centers at a time, making =A0 23 passes doing = MaxLOS=3D2.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D =A0 0= AccDes=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent= =3D =A0 0 AccDes=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D =A0 0 AccDes=3D 0.00= D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D =A0 0 AccDes=3D 0.00= D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D =A0 0 AccDe= s=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D = =A0 0 AccDes=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I= 1Cent=3D =A0 0 AccDes=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D =A0 0 AccDes=3D 0.00= D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D =A0 0 AccDe= s=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D = =A0 0 AccDes=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I= 1Cent=3D =A0 0 AccDes=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D =A0 0 AccDes=3D 0.00= D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D =A0 0 AccDe= s=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D = =A0 0 AccDes=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I= 1Cent=3D =A0 0 AccDes=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D =A0 0 AccDes=3D 0.00= D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D =A0 0 AccDe= s=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D = =A0 0 AccDes=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I= 1Cent=3D =A0 0 AccDes=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D =A0 0 AccDes=3D 0.00= D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D =A0 0 AccDe= s=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I1Cent=3D = =A0 0 AccDes=3D 0.00D+00.
=A0Calling FoFCou, ICntrl=3D =A03107 FMM=3DT I= 1Cent=3D =A0 0 AccDes=3D 0.00D+00.
=A0FoFDir/FoFCou used for L=3D0 through L=3D2.
=A0End of G2Drv Frequency= -dependent properties file =A0 721 does not exist.
=A0End of G2Drv Frequ= ency-dependent properties file =A0 722 does not exist.
=A0 =A0 =A0 =A0 = =A0IDoAtm=3D11111111111111111111111111111111111111111111111111
=A0 =A0 =A0 =A0 =A0IDoAtm=3D11111111111111111111111111111111111111
=A0 = =A0 =A0 =A0 =A0Differentiating once with respect to electric field.
=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0with respect to dipole field.
=A0 =A0 =A0 =A0= =A0Differentiating once with respect to nuclear coordinates.
=A0 =A0 =A0 =A0 =A0There are =A0 267 degrees of freedom in the 1st order CP= HF. =A0IDoFFX=3D5.
=A0 =A0267 vectors produced by pass =A00 Test12=3D 1.= 53D-13 1.00D-09 XBig12=3D 3.87D+02 6.76D+00.
=A0AX will form =A0 =A015 A= O Fock derivatives at one time.
=A0 =A0267 vectors produced by pass =A01 Test12=3D 1.53D-13 1.00D-09 XBig12= =3D 8.56D+01 1.11D+00.
=A0 =A0264 vectors produced by pass =A02 Test12= =3D 1.53D-13 1.00D-09 XBig12=3D 5.91D-01 5.93D-02.
=A0 =A0264 vectors pr= oduced by pass =A03 Test12=3D 1.53D-13 1.00D-09 XBig12=3D 2.23D-03 3.14D-03= .
=A0 =A0264 vectors produced by pass =A04 Test12=3D 1.53D-13 1.00D-09 XBig12= =3D 4.09D-06 1.29D-04.
=A0 =A0264 vectors produced by pass =A05 Test12= =3D 1.53D-13 1.00D-09 XBig12=3D 6.15D-09 4.16D-06.
=A0 =A0258 vectors pr= oduced by pass =A06 Test12=3D 1.53D-13 1.00D-09 XBig12=3D 1.40D-11 2.66D-07= .
=A0 =A0236 vectors produced by pass =A07 Test12=3D 1.53D-13 1.00D-09 XBig12= =3D 5.06D-13 2.87D-08.
=A0 =A0219 vectors produced by pass =A08 Test12= =3D 1.53D-13 1.00D-09 XBig12=3D 2.56D-14 6.21D-09.
=A0 =A0199 vectors pr= oduced by pass =A09 Test12=3D 1.53D-13 1.00D-09 XBig12=3D 2.12D-14 5.20D-09= .
=A0 =A0177 vectors produced by pass 10 Test12=3D 1.53D-13 1.00D-09 XBig12= =3D 2.01D-14 5.01D-09.
=A0Internal consistency error detected in FileIO = for unit 1 I=3D =A0 7 J=3D =A0 0 IFail=3D 1.


=A0dumping /fiocom/= , unit =3D 1 NFiles =3D =A0 =A088 SizExt =3D =A0 =A0 32768 WInBlk =3D =A0 = =A0 =A0 512
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 defal =3D F LstWrd =3D -1962280960 FTyp= e=3D2 FMxFil=3D10000

=A0Number =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A0= =A00 =A0 =A0 =A0 =A0 =A00 =A0 =A0 =A0 =A0 =A00 =A0 =A0 =A0 =A0 =A00 =A0 = =A0 =A0 =A0 =A00 =A0 =A0 =A0 =A0 =A00 =A0 =A0 =A0 =A0501
=A0Base =A0 =A0= =A011258363 =A0 10315776 =A0 73707520 =A0 18034688 =A0 11021824 =A03629941= 76-1962321632 =A0 =A0 =A023552
=A0End =A0 =A0 =A0 11720192 =A0 10317312 =A0 92399104 =A0 22244864 =A0 1102= 3360 =A0772379936-1962280960 =A0 =A0 =A024552
=A0End1 =A0 =A0 =A01172019= 2 =A0 10317312 =A0 92399104 =A0 22244864 =A0 11023360 =A0772379936-19622809= 60 =A0 =A0 =A024576
=A0Wr Pntr =A0 11258363 =A0 10315776 =A0 73707520 = =A0 18034688 =A0 11021824 =A0362994176 1757205680 =A0 =A0 =A023552
=A0Rd Pntr =A0 11258363 =A0 10315776 =A0 73707520 =A0 18034688 =A0 11021824= =A0362994176 1757205680 =A0 =A0 =A023552
=A0Length =A0 =A0 =A0461829 = =A0 =A0 =A0 1536 =A0 18691584 =A0 =A04210176 =A0 =A0 =A0 1536 =A0409385760 = =A0 =A0 =A040672 =A0 =A0 =A0 1000

=A0Number =A0 =A0 =A0 =A0 502 =A0 = =A0 =A0 =A0503 =A0 =A0 =A0 =A0507 =A0 =A0 =A0 =A0508 =A0 =A0 =A0 =A0511 =A0= =A0 =A0 =A0514 =A0 =A0 =A0 =A0515 =A0 =A0 =A0 =A0516
=A0Base =A0 =A0 =A0 =A0275968 =A0 =A0 =A096256 =A0 =A0 =A097280 =A0 =A0 284= 160 =A0 =A0 225280 =A0 =A05214208 =A0 =A02407936 =A0 =A0 303104
=A0End = =A0 =A0 =A0 =A0 279797 =A0 =A0 =A096829 =A0 =A0 =A098033 =A0 =A0 284175 =A0= =A0 260526 =A0 =A05915728 =A0 =A05214016 =A0 =A02407664
=A0End1 =A0 =A0= =A0 =A0280064 =A0 =A0 =A097280 =A0 =A0 =A098304 =A0 =A0 284672 =A0 =A0 260= 608 =A0 =A05916160 =A0 =A05214208 =A0 =A02407936
=A0Wr Pntr =A0 =A0 275968 =A0 =A0 =A096256 =A0 =A0 =A097280 =A0 =A0 284160 = =A0 =A0 225280 =A0 =A05214208 =A0 =A02407936 =A0 =A0 303104
=A0Rd Pntr = =A0 =A0 275968 =A0 =A0 =A096256 =A0 =A0 =A097280 =A0 =A0 284160 =A0 =A0 225= 280 =A0 =A05214208 =A0 =A02407936 =A0 =A0 303104
=A0Length =A0 =A0 =A0 = =A03829 =A0 =A0 =A0 =A0573 =A0 =A0 =A0 =A0753 =A0 =A0 =A0 =A0 15 =A0 =A0 = =A035246 =A0 =A0 701520 =A0 =A02806080 =A0 =A02104560

=A0Number =A0 =A0 =A0 =A0 517 =A0 =A0 =A0 =A0518 =A0 =A0 =A0 =A0520 =A0= =A0 =A0 =A0521 =A0 =A0 =A0 =A0522 =A0 =A0 =A0 =A0523 =A0 =A0 =A0 =A0524 = =A0 =A0 =A0 =A0526
=A0Base =A0 =A0 =A010208768 =A0 =A08103936 =A0 =A0 30= 1568 =A0 =A0 268800 =A0 11019264 =A0 10313216 =A0 11720192 =A0 14526976
= =A0End =A0 =A0 =A0 10312960 =A0 10208496 =A0 =A0 301573 =A0 =A0 268835 =A0 = 11021632 =A0 10315584 =A0 13122048 =A0 15928832
=A0End1 =A0 =A0 =A010313216 =A0 10208768 =A0 =A0 302080 =A0 =A0 269312 =A0 = 11021824 =A0 10315776 =A0 13122048 =A0 15928832
=A0Wr Pntr =A0 10208768 = =A0 =A08103936 =A0 =A0 301568 =A0 =A0 268800 =A0 11019264 =A0 10313216 =A0 = 11720192 =A0 14526976
=A0Rd Pntr =A0 10208768 =A0 =A08103936 =A0 =A0 301= 568 =A0 =A0 268800 =A0 11019264 =A0 10313216 =A0 11720192 =A0 14526976
=A0Length =A0 =A0 =A0104192 =A0 =A02104560 =A0 =A0 =A0 =A0 =A05 =A0 =A0 =A0= =A0 35 =A0 =A0 =A0 2368 =A0 =A0 =A0 2368 =A0 =A01401856 =A0 =A01401856
=
=A0Number =A0 =A0 =A0 =A0 528 =A0 =A0 =A0 =A0530 =A0 =A0 =A0 =A0532 =A0= =A0 =A0 =A0534 =A0 =A0 =A0 =A0536 =A0 =A0 =A0 =A0538 =A0 =A0 =A0 =A0545 = =A0 =A0 =A0 =A0547
=A0Base =A0 =A0 =A013122048 =A0 10317312 =A0 13825024= =A0 15928832 =A0 16630784 =A0 17332736 =A0 11025408 =A0 11026944
=A0End =A0 =A0 =A0 13823568 =A0 11018832 =A0 14526544 =A0 16630352 =A0 1733= 2304 =A0 18034256 =A0 11025422 =A0 11029312
=A0End1 =A0 =A0 =A013824000 = =A0 11019264 =A0 14526976 =A0 16630784 =A0 17332736 =A0 18034688 =A0 110259= 20 =A0 11029504
=A0Wr Pntr =A0 13122048 =A0 10317312 =A0 13825024 =A0 15= 928832 =A0 16630784 =A0 17332736 =A0 11025408 =A0 11026944
=A0Rd Pntr =A0 13122048 =A0 10317312 =A0 13825024 =A0 15928832 =A0 16630784= =A0 17332736 =A0 11025408 =A0 11026944
=A0Length =A0 =A0 =A0701520 =A0 = =A0 701520 =A0 =A0 701520 =A0 =A0 701520 =A0 =A0 701520 =A0 =A0 701520 =A0 = =A0 =A0 =A0 14 =A0 =A0 =A0 2368

=A0Number =A0 =A0 =A0 =A0 548 =A0 = =A0 =A0 =A0551 =A0 =A0 =A0 =A0552 =A0 =A0 =A0 =A0559 =A0 =A0 =A0 =A0562 =A0= =A0 =A0 =A0563 =A0 =A0 =A0 =A0565 =A0 =A0 =A0 =A0569
=A0Base =A0 =A0 =A022946816 =A0 =A0 267264 =A0 =A0 =A022016 =A0 =A0 =A04300= 8 =A0 =A0 260608 =A0 13824000 =A0 =A0 283648 =A0 11024896
=A0End =A0 =A0= =A0 24348672 =A0 =A0 267289 =A0 =A0 =A022032 =A0 =A0 =A043009 =A0 =A0 2665= 45 =A0 13824592 =A0 =A0 283865 =A0 11024897
=A0End1 =A0 =A0 =A024348672 = =A0 =A0 267776 =A0 =A0 =A022528 =A0 =A0 =A043520 =A0 =A0 266752 =A0 1382502= 4 =A0 =A0 284160 =A0 11025408
=A0Wr Pntr =A0 22946816 =A0 =A0 267264 =A0 =A0 =A022016 =A0 =A0 =A043008 = =A0 =A0 260608 =A0 13824000 =A0 =A0 283648 =A0 11024896
=A0Rd Pntr =A0 2= 2946816 =A0 =A0 267264 =A0 =A0 =A022016 =A0 =A0 =A043008 =A0 =A0 260608 =A0= 13824000 =A0 =A0 283648 =A0 11024896
=A0Length =A0 =A0 1401856 =A0 =A0 = =A0 =A0 25 =A0 =A0 =A0 =A0 16 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 5937 =A0 =A0= =A0 =A0592 =A0 =A0 =A0 =A0217 =A0 =A0 =A0 =A0 =A01

=A0Number =A0 =A0 =A0 =A0 571 =A0 =A0 =A0 =A0575 =A0 =A0 =A0 =A0577 =A0= =A0 =A0 =A0579 =A0 =A0 =A0 =A0580 =A0 =A0 =A0 =A0581 =A0 =A0 =A0 =A0582 = =A0 =A0 =A0 =A0583
=A0Base =A0 =A0 =A022244864 =A0 =A0 100864 =A0 =A0 28= 2112 =A0 =A0 266752 =A0 =A0 =A041472 =A0 =A0 282624 =A0 =A0 280064 =A0 =A0 = =A043520
=A0End =A0 =A0 =A0 22946384 =A0 =A0 225207 =A0 =A0 282138 =A0 = =A0 266796 =A0 =A0 =A042677 =A0 =A0 283248 =A0 =A0 281840 =A0 =A0 =A043565<= br> =A0End1 =A0 =A0 =A022946816 =A0 =A0 225280 =A0 =A0 282624 =A0 =A0 267264 = =A0 =A0 =A043008 =A0 =A0 283648 =A0 =A0 282112 =A0 =A0 =A044032
=A0Wr Pn= tr =A0 22244864 =A0 =A0 100864 =A0 =A0 282112 =A0 =A0 266752 =A0 =A0 =A0414= 72 =A0 =A0 282624 =A0 =A0 280064 =A0 =A0 =A043520
=A0Rd Pntr =A0 2224486= 4 =A0 =A0 100864 =A0 =A0 282112 =A0 =A0 266752 =A0 =A0 =A041472 =A0 =A0 282= 624 =A0 =A0 280064 =A0 =A0 =A043520
=A0Length =A0 =A0 =A0701520 =A0 =A0 124343 =A0 =A0 =A0 =A0 26 =A0 =A0 =A0 = =A0 44 =A0 =A0 =A0 1205 =A0 =A0 =A0 =A0624 =A0 =A0 =A0 1776 =A0 =A0 =A0 =A0= 45

=A0Number =A0 =A0 =A0 =A0 584 =A0 =A0 =A0 =A0588 =A0 =A0 =A0 =A0= 590 =A0 =A0 =A0 =A0598 =A0 =A0 =A0 =A0600 =A0 =A0 =A0 =A0603 =A0 =A0 =A0 = =A0605 =A0 =A0 =A0 =A0606
=A0Base =A0 =A0 =A0 =A0284672 =A0 24348672 =A0= 93810176 =A0 =A0 =A044032 =A0 11103744 =A0 =A0 302080 =A0 =A0 302592 =A0 1= 1023360
=A0End =A0 =A0 =A0 =A0 285200 =A0 26453232 =A0281116016 =A0 =A0 =A044034 = =A0 11104647 =A0 =A0 302081 =A0 =A0 302593 =A0 11024544
=A0End1 =A0 =A0 = =A0 =A0285696 =A0 26453504 =A0281116160 =A0 =A0 =A044544 =A0 11104768 =A0 = =A0 302592 =A0 =A0 303104 =A0 11024896
=A0Wr Pntr =A0 =A0 284672 =A0 243= 48672 =A0 93810176 =A0 =A0 =A044032 =A0 11103744 =A0 =A0 302080 =A0 =A0 302= 592 =A0 11023360
=A0Rd Pntr =A0 =A0 284672 =A0 24348672 =A0 93810176 =A0 =A0 =A044032 =A0 11= 103744 =A0 =A0 302080 =A0 =A0 302592 =A0 11023360
=A0Length =A0 =A0 =A0 = =A0 528 =A0 =A02104560 =A0187305840 =A0 =A0 =A0 =A0 =A02 =A0 =A0 =A0 =A0903= =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 =A0 =A01 =A0 =A0 =A0 1184

=A0Numbe= r =A0 =A0 =A0 =A0 607 =A0 =A0 =A0 =A0619 =A0 =A0 =A0 =A0634 =A0 =A0 =A0 =A0= 670 =A0 =A0 =A0 =A0674 =A0 =A0 =A0 =A0685 =A0 =A0 =A0 =A0694 =A0 =A0 =A0 = =A0695
=A0Base =A0 =A0 =A011025920 =A0 =A0 285696 =A0 92399104 =A0 =A0 269312 =A0 = =A0 =A098304 =A0 =A05916160 =A0 11029504 =A0 =A0 298496
=A0End =A0 =A0 = =A0 11026512 =A0 =A0 298421 =A0 93809785 =A0 =A0 275761 =A0 =A0 =A098936 = =A0 =A07318016 =A0 11031872 =A0 =A0 301252
=A0End1 =A0 =A0 =A011026944 = =A0 =A0 298496 =A0 93810176 =A0 =A0 275968 =A0 =A0 =A099328 =A0 =A07318016 = =A0 11032064 =A0 =A0 301568
=A0Wr Pntr =A0 11025920 =A0 =A0 285696 =A0 92399104 =A0 =A0 269312 =A0 =A0 = =A098304 =A0 =A05916160 =A0 11029504 =A0 =A0 298496
=A0Rd Pntr =A0 11025= 920 =A0 =A0 285696 =A0 92399104 =A0 =A0 269312 =A0 =A0 =A098304 =A0 =A05916= 160 =A0 11029504 =A0 =A0 298496
=A0Length =A0 =A0 =A0 =A0 592 =A0 =A0 = =A012725 =A0 =A01410681 =A0 =A0 =A0 6449 =A0 =A0 =A0 =A0632 =A0 =A01401856 = =A0 =A0 =A0 2368 =A0 =A0 =A0 2756

=A0Number =A0 =A0 =A0 =A0 698 =A0 =A0 =A0 =A0742 =A0 =A0 =A0 =A0989 =A0= =A0 =A0 =A0991 =A0 =A0 =A0 =A0992 =A0 =A0 =A0 =A0993 =A0 =A0 =A0 =A0994 = =A0 =A0 =A0 =A0995
=A0Base =A0 =A0 =A0 =A0267776 =A0 =A07318016 =A0 =A0 = =A024576 =A0 =A0 =A037888 =A0 =A0 =A037376 =A0 =A0 =A023040 =A0 =A0 =A02048= 0 =A0 =A0 =A022528
=A0End =A0 =A0 =A0 =A0 268304 =A0 =A08103928 =A0 =A0 = =A037076 =A0 =A0 =A041169 =A0 =A0 =A037381 =A0 =A0 =A023140 =A0 =A0 =A02051= 0 =A0 =A0 =A022538
=A0End1 =A0 =A0 =A0 =A0268800 =A0 =A08103936 =A0 =A0 =A037376 =A0 =A0 =A041= 472 =A0 =A0 =A037888 =A0 =A0 =A023552 =A0 =A0 =A020992 =A0 =A0 =A023040
= =A0Wr Pntr =A0 =A0 267776 =A0 =A07318016 =A0 =A0 =A024576 =A0 =A0 =A037888 = =A0 =A0 =A037376 =A0 =A0 =A023040 =A0 =A0 =A020480 =A0 =A0 =A022528
=A0R= d Pntr =A0 =A0 267776 =A0 =A07318016 =A0 =A0 =A024576 =A0 =A0 =A037888 =A0 = =A0 =A037376 =A0 =A0 =A023040 =A0 =A0 =A020480 =A0 =A0 =A022528
=A0Length =A0 =A0 =A0 =A0 528 =A0 =A0 785912 =A0 =A0 =A012500 =A0 =A0 =A0 3= 281 =A0 =A0 =A0 =A0 =A05 =A0 =A0 =A0 =A0100 =A0 =A0 =A0 =A0 30 =A0 =A0 =A0 = =A0 10

=A0Number =A0 =A0 =A0 =A0 996 =A0 =A0 =A0 =A0997 =A0 =A0 =A0 = =A0998 =A0 =A0 =A0 =A0999 =A0 =A0 =A0 2999 =A0 =A0 =A0 3001 =A0 =A0 =A0 300= 3 =A0 =A0 =A0 3005
=A0Base =A0 =A0 =A0 =A0 21504 =A0 =A0 =A099328 =A0 = =A0 =A020992 =A0 =A0 =A044544 =A0 11032064 =A0 28558848 =A0281116160 =A0 69= 497856
=A0End =A0 =A0 =A0 =A0 =A021604 =A0 =A0 100571 =A0 =A0 =A021192 =A0 =A0 =A0= 95796 =A0 11103353 =A0 69497424 =A0322054736 =A0 71602416
=A0End1 =A0 = =A0 =A0 =A0 22016 =A0 =A0 100864 =A0 =A0 =A021504 =A0 =A0 =A096256 =A0 1110= 3744 =A0 69497856 =A0322055168 =A0 71602688
=A0Wr Pntr =A0 =A0 =A021504 = =A0 =A0 =A099328 =A0 =A0 =A020992 =A0 =A0 =A044544 =A0 11032064 =A0 2855884= 8 =A0281116160 =A0 69497856
=A0Rd Pntr =A0 =A0 =A021504 =A0 =A0 =A099328 =A0 =A0 =A020992 =A0 =A0 =A044= 544 =A0 11032064 =A0 28558848 =A0281116160 =A0 69497856
=A0Length =A0 = =A0 =A0 =A0 100 =A0 =A0 =A0 1243 =A0 =A0 =A0 =A0200 =A0 =A0 =A051252 =A0 = =A0 =A071289 =A0 40938576 =A0 40938576 =A0 =A02104560

=A0Number =A0 = =A0 =A0 =A03007 =A0 =A0 =A0 3026 =A0 =A0 =A0 9994 =A0 =A0 =A0 9995 =A0 =A0 = =A0 9996 =A0 =A0 =A0 9997 =A0 =A0 =A0 9998 =A0 =A0 =A0 9999
=A0Base =A0 =A0 =A071602688 =A0 27856896 1181765696 =A0772379936 1757205680= =A0 11104768 =A0322055168 =A0 26453504
=A0End =A0 =A0 =A0 73707248 =A0 = 28558416 1757205680 1181765696-1962321632 =A0 11258363 =A0362993744 =A0 278= 56544
=A0End1 =A0 =A0 =A073707520 =A0 28558848 1757205680 1181765696-196= 2321632 =A0 11258363 =A0362994176 =A0 27856896
=A0Wr Pntr =A0 71602688 =A0 27856896 1181765696 =A0772379936 1757205680 =A0= 11104768 =A0322055168 =A0 26453504
=A0Rd Pntr =A0 71602688 =A0 27856896= 1181765696 =A0772379936 1757205680 =A0 11104768 =A0322055168 =A0 26453504<= br>=A0Length =A0 =A0 2104560 =A0 =A0 701520 =A0575439984 =A0409385760 =A057= 5439984 =A0 =A0 153595 =A0 40938576 =A0 =A01403040


=A0dumping /fiocom/, unit =3D 2 NFiles =3D =A0 =A0 7 SizExt =3D =A0= =A0 =A0 =A0 0 WInBlk =3D =A0 =A0 =A0 512
=A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 =A0 defal =3D F LstWrd =3D =A0 =A0 2838528 FType=3D2 FMxFil=3D10000
=
=A0Number =A0 =A0 =A0 =A0 =A0 0 =A0 =A0 =A0 =A0508 =A0 =A0 =A0 =A0522 = =A0 =A0 =A0 =A0536 =A0 =A0 =A0 =A0538 =A0 =A0 =A0 =A0634 =A0 =A0 =A0 =A0998=
=A0Base =A0 =A0 =A0 2836784 =A0 =A0 =A020480 =A0 =A0 =A020695 =A0 =A0143374= 4 =A0 =A02135264 =A0 =A0 =A023063 =A0 =A0 =A020495
=A0End =A0 =A0 =A0 = =A02838528 =A0 =A0 =A020495 =A0 =A0 =A023063 =A0 =A02135264 =A0 =A02836784 = =A0 =A01433744 =A0 =A0 =A020695
=A0End1 =A0 =A0 =A0 2838528 =A0 =A0 =A02= 0495 =A0 =A0 =A023063 =A0 =A02135264 =A0 =A02836784 =A0 =A01433744 =A0 =A0 = =A020695
=A0Wr Pntr =A0 =A02836784 =A0 =A0 =A020480 =A0 =A0 =A020695 =A0 =A01433744 = =A0 =A02135264 =A0 =A0 =A023063 =A0 =A0 =A020495
=A0Rd Pntr =A0 =A028367= 84 =A0 =A0 =A020480 =A0 =A0 =A020695 =A0 =A01433744 =A0 =A02135264 =A0 =A0 = =A023063 =A0 =A0 =A020495
=A0Length =A0 =A0 =A0 =A01744 =A0 =A0 =A0 =A0 = 15 =A0 =A0 =A0 2368 =A0 =A0 701520 =A0 =A0 701520 =A0 =A01410681 =A0 =A0 = =A0 =A0200


=A0dumping /fiocom/, unit =3D 3 NFiles =3D =A0 =A0 1 SizExt =3D =A0= =A0524288 WInBlk =3D =A0 =A0 =A0 512
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = =A0 defal =3D T LstWrd =3D =A0 =A0 =A0 67072 FType=3D2 FMxFil=3D10000
=A0Number =A0 =A0 =A0 =A0 =A0 0
=A0Base =A0 =A0 =A0 =A0 20480
=A0En= d =A0 =A0 =A0 =A0 =A067072
=A0End1 =A0 =A0 =A0 =A0 67072
=A0Wr Pntr =A0 =A0 =A020480
=A0Rd Pntr = =A0 =A0 =A020480
=A0Length =A0 =A0 =A0 46592
=A0Error termination in = NtrErr:
=A0NtrErr called from FIOCnC.

Can anybody tell me that wh= at is the problem in my calculation and why it is coming and what is its so= lution? Thank you very much in advance.
With regards,
Vijay Tak



-=3D This is automatically added = to each message by the mailing script =3D-
To recover the email address = of the author of the message, please change
the strange characters on th= e top line to the ^ sign. You can also
E-mail to subs= cribers: CHEMISTRY^ccl.net or use:=
=A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: = CHEMISTRY-REQUEST^ccl.net or use
=A0 =A0 =A0http://www.ccl.net/cg= i-bin/ccl/send_ccl_message

Subscribe/Unsubscribe:
=A0 =A0 =A0http://www.ccl.net/chemistry/sub_u= nsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.c= cl.net/jobs
Conferences: http://server.ccl.net/chemist= ry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.sht= ml
=A0= =A0 =A0http:= //www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/


--0016e6d971090475b3049749172e-- From owner-chemistry@ccl.net Mon Dec 13 15:11:00 2010 From: "David Mannock dmannock _ ualberta.ca" To: CCL Subject: CCL: software for selective alignment of different elements of the small molecules Message-Id: <-43375-101213141404-25587-JbmysGzLgSMkXNqIi9yUSQ:-:server.ccl.net> X-Original-From: David Mannock Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 13 Dec 2010 12:13:54 -0700 MIME-Version: 1.0 Sent to CCL by: David Mannock [dmannock{=}ualberta.ca] Andrey, I have recently done this with a set of sterol side-chain conformers and used DSvisualizer 2.X or DS viewerpro 6.0 using a semi-automatic method for conformations generated by Verachem's Vconf. Go to align structures and add tethers to the key parts of the molecule in the region that you want to overlay. I have overlaid many molecules very accurately using this method. There is not much need for tweaking the results if the points are correctly chosen. OS is MS WinXP in my case. Dave On 11/12/2010 1:30 PM, Andrew Voronkov drugdesign*yandex.ru wrote: > Sent to CCL by: Andrew Voronkov [drugdesign-x-yandex.ru] > > Dear CCL users, > I'd like to find the software for alignment of the selected small molecule elements. For example I have a series of conformations and I am getting alignment with one shared element, while I'd like to try to use another. Let's say I have parts A, B, C, D and E and I want to get parts D and E alignmed so that I can see the differences in parts A and B orientation. Can you please recommend software packages which can help me to do selective alignment? > > It would be nice to use something free or with evaluation version. > > > > Sincerely yours, > Andrey> > > > From owner-chemistry@ccl.net Mon Dec 13 15:47:01 2010 From: "Jamin Krinsky krinsky.jamin[A]gmail.com" To: CCL Subject: CCL:G: Problem in Guassian freq calculation Message-Id: <-43376-101213145155-18022-ftJKOUwlFLBFyDKJ/RP3bg*server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 13 Dec 2010 11:51:16 -0800 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [krinsky.jamin^gmail.com] Hi Vijay, It looks like what is actually happening is that the CPHF step is not converging. I've seen this before and the Gaussian people suggested tightening up the integral accuracies for this step, using Int=Acc2E=11 (I think the default is 10). This has worked for me, but of course the calculation takes longer. With that basis set I would also use a tighter grid, so the keyword would be int=(ultrafinegrid,acc2e=11) (note that that is the G09 syntax, doesn't work with G03). Regards, Jamin On Sun, Dec 12, 2010 at 11:34 PM, Vijay Kumar Tak takvijay*|*gmail.com wrote: > > Sent to CCL by: "Vijay Kumar Tak" [takvijay!=!gmail.com] > Hello, > There is a problem in calculating the frequency of an compund carrying a three positive chages. I have optimized the conformation of trication which consist of 88 atoms at B3LYP level. Then  i am trying to calculate the frequency of same conformation at the same level, but the out  put file is showing following error. >  ****************************************** >  Gaussian 09:  IA32W-G09RevA.02 11-Jun-2009 >                11-Dec-2010 >  ****************************************** >  %nprocshared=8 >  Will use up to    8 processors via shared memory. >  %mem=1GB >  %chk=E:\Guassian calculations\Trication\DFT-B3LYP\1Freq.chk >  --------------------------------------------------------------- >  # freq=noraman cphf=noread b3lyp/6-311+g(d,p) geom=connectivity >  --------------------------------------------------------------- >  1/10=4,30=1,38=1,57=2/1,3; >  2/12=2,17=6,18=5,40=1/2; >  3/5=4,6=6,7=111,11=2,16=1,25=1,30=1,71=2,74=-5/1,2,3; >  4//1; >  5/5=2,38=5,98=1/2; >  8/6=4,10=90,11=11/1; >  11/6=1,8=1,9=11,15=111,16=1/1,2,10; >  10/6=1/2; >  6/7=2,8=2,9=2,10=2,18=1,28=1/1; >  7/8=1,10=1,25=1/1,2,3,16; >  1/10=4,30=1/3; >  99//99; >  ----- >  1Freq >  ----- >  Symbolic Z-matrix: >  Charge =  3 Multiplicity = 1 >  C                    -14.05514  -0.30777   1.48727 >  C                    -14.84798   0.78786   1.83187 >  C                    -14.72668   1.98553   1.1309 >  C                    -13.80815   2.09126   0.08739 >  C                    -13.00564   0.99913  -0.25784 >  C                    -13.13873  -0.20414   0.4453 >  C                    -12.02369   1.11721  -1.39256 >  N                    -10.61123   1.31574  -0.91687 >  C                    -10.21931   2.04802   0.18506 >  C                    -8.85798   2.0396    0.21013 >  N                    -8.43244   1.29947  -0.87866 >  C                    -9.51721   0.87568  -1.54268 >  C                    -7.02846   1.03252  -1.25739 >  C                    -6.31137   0.08478  -0.28811 >  C                    -4.85723  -0.17144  -0.71843 >  C                    -4.1112   -1.10244   0.25006 >  C                    -2.66345  -1.3933   -0.18343 >  C                    -1.98338  -2.34883   0.80213 >  N                    -0.59636  -2.72048   0.42241 >  C                     0.49117  -2.54755   1.18283 >  N                     1.54931  -3.0916    0.57002 >  C                     1.11896  -3.63833  -0.62513 >  C                    -0.21873  -3.40475  -0.71828 >  C                     2.90508  -3.24005   1.16662 >  C                     4.05788  -2.79091   0.26352 >  C                     4.15705  -1.27597   0.03719 >  C                     5.32799  -0.84492  -0.86707 >  C                     6.72808  -1.03907  -0.25782 >  C                     7.81353  -0.50618  -1.20285 >  N                     9.18436  -0.67399  -0.67628 >  C                     9.99921   0.31757  -0.28677 >  N                     11.16496  -0.20587   0.09609 >  C                     11.09966  -1.57792  -0.05343 >  C                     9.86287  -1.87229  -0.53766 >  C                     12.36011   0.5472    0.60983 >  C                     12.2046   2.03928   0.49535 >  C                     11.72322   2.78352   1.5785 >  C                     11.59043   4.167     1.47547 >  C                     11.93896   4.81416   0.29083 >  C                     12.42509   4.07915  -0.79052 >  C                     12.55974   2.69678  -0.68887 >  H                    -14.16351  -1.24468   2.02048 >  H                    -15.56841   0.70225   2.63662 >  H                    -15.35334   2.83171   1.38566 >  H                    -13.73327   3.01981  -0.46991 >  H                    -12.54067  -1.06719   0.16897 >  H                    -12.00763   0.21677  -2.00834 >  H                    -12.26274   1.9685   -2.0319 >  H                    -10.93532   2.49789   0.85127 >  H                    -8.17029   2.4977    0.90001 >  H                    -9.50739   0.28436  -2.44346 >  H                    -7.04881   0.61717  -2.26637 >  H                    -6.52158   1.99845  -1.3126 >  H                    -6.32711   0.51258   0.71968 >  H                    -6.8596   -0.86175  -0.23853 >  H                    -4.8469   -0.60934  -1.72349 >  H                    -4.32286   0.78307  -0.79029 >  H                    -4.10859  -0.65585   1.2512 >  H                    -4.65934  -2.04799   0.33501 >  H                    -2.66532  -1.83432  -1.18567 >  H                    -2.091    -0.46202  -0.2448 >  H                    -1.92252  -1.90434   1.79676 >  H                    -2.54458  -3.28181   0.8931 >  H                     0.50778  -2.06831   2.14791 >  H                     1.78181  -4.15552  -1.29704 >  H                    -0.92084  -3.67961  -1.48655 >  H                     2.89481  -2.66901   2.09656 >  H                     3.01414  -4.29509   1.42588 >  H                     4.96385  -3.16166   0.75273 >  H                     4.00588  -3.31629  -0.69665 >  H                     4.23916  -0.76778   1.00571 >  H                     3.23041  -0.9144   -0.42205 >  H                     5.19336   0.21456  -1.10873 >  H                     5.26553  -1.38324  -1.82042 >  H                     6.91735  -2.09782  -0.05506 >  H                     6.79544  -0.51358   0.70079 >  H                     7.67679   0.56031  -1.38848 >  H                     7.77557  -1.01238  -2.17006 >  H                     9.76587   1.3689   -0.29299 >  H                     11.93069  -2.22061   0.18476 >  H                     9.4258   -2.81868  -0.80634 >  H                     13.21073   0.18858   0.02858 >  H                     12.49515   0.23879   1.64769 >  H                     11.477    2.28761   2.51228 >  H                     11.23562   4.73975   2.32397 >  H                     11.85051   5.89153   0.21621 >  H                     12.71813   4.58395  -1.70328 >  H                     12.96438   2.13382  -1.52421 > > >  GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad >  Berny optimization. >  Initialization pass. >  Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 >  Number of steps in this run=   2 maximum allowed number of steps=   2. >  GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad > >  Stoichiometry    C35H47N6(3+) >  Framework group  C1[X(C35H47N6)] >  Deg. of freedom   258 >  Full point group                 C1      NOp   1 >  Largest Abelian subgroup         C1      NOp   1 >  Largest concise Abelian subgroup C1      NOp   1 >                         Standard orientation: >  --------------------------------------------------------------------- >  Center     Atomic      Atomic             Coordinates (Angstroms) >  Number     Number       Type             X           Y           Z >  --------------------------------------------------------------------- >      1          6           0      -14.055140   -0.307766    1.487270 >      2          6           0      -14.847981    0.787858    1.831866 >      3          6           0      -14.726677    1.985534    1.130895 >      4          6           0      -13.808148    2.091260    0.087392 >      5          6           0      -13.005645    0.999125   -0.257839 >      6          6           0      -13.138734   -0.204138    0.445304 >      7          6           0      -12.023692    1.117210   -1.392560 >      8          7           0      -10.611225    1.315743   -0.916872 >      9          6           0      -10.219311    2.048020    0.185057 >     10          6           0       -8.857979    2.039598    0.210133 >     11          7           0       -8.432440    1.299473   -0.878655 >     12          6           0       -9.517207    0.875681   -1.542684 >     13          6           0       -7.028455    1.032515   -1.257391 >     14          6           0       -6.311368    0.084778   -0.288110 >     15          6           0       -4.857232   -0.171438   -0.718427 >     16          6           0       -4.111197   -1.102435    0.250063 >     17          6           0       -2.663446   -1.393301   -0.183430 >     18          6           0       -1.983377   -2.348833    0.802131 >     19          7           0       -0.596363   -2.720478    0.422409 >     20          6           0        0.491172   -2.547550    1.182831 >     21          7           0        1.549314   -3.091600    0.570022 >     22          6           0        1.118956   -3.638332   -0.625134 >     23          6           0       -0.218727   -3.404747   -0.718276 >     24          6           0        2.905076   -3.240050    1.166616 >     25          6           0        4.057883   -2.790909    0.263519 >     26          6           0        4.157045   -1.275970    0.037194 >     27          6           0        5.327988   -0.844917   -0.867068 >     28          6           0        6.728078   -1.039068   -0.257817 >     29          6           0        7.813525   -0.506180   -1.202848 >     30          7           0        9.184359   -0.673991   -0.676284 >     31          6           0        9.999211    0.317569   -0.286767 >     32          7           0       11.164957   -0.205873    0.096087 >     33          6           0       11.099655   -1.577922   -0.053427 >     34          6           0        9.862871   -1.872290   -0.537662 >     35          6           0       12.360109    0.547195    0.609832 >     36          6           0       12.204601    2.039279    0.495350 >     37          6           0       11.723218    2.783523    1.578500 >     38          6           0       11.590427    4.166996    1.475465 >     39          6           0       11.938956    4.814158    0.290826 >     40          6           0       12.425085    4.079151   -0.790522 >     41          6           0       12.559738    2.696778   -0.688870 >     42          1           0      -14.163506   -1.244678    2.020477 >     43          1           0      -15.568414    0.702249    2.636615 >     44          1           0      -15.353339    2.831712    1.385663 >     45          1           0      -13.733274    3.019809   -0.469909 >     46          1           0      -12.540668   -1.067191    0.168965 >     47          1           0      -12.007630    0.216772   -2.008343 >     48          1           0      -12.262742    1.968498   -2.031902 >     49          1           0      -10.935324    2.497886    0.851274 >     50          1           0       -8.170292    2.497702    0.900012 >     51          1           0       -9.507394    0.284364   -2.443457 >     52          1           0       -7.048810    0.617168   -2.266372 >     53          1           0       -6.521579    1.998451   -1.312597 >     54          1           0       -6.327105    0.512579    0.719675 >     55          1           0       -6.859602   -0.861749   -0.238533 >     56          1           0       -4.846899   -0.609341   -1.723485 >     57          1           0       -4.322863    0.783067   -0.790291 >     58          1           0       -4.108592   -0.655852    1.251203 >     59          1           0       -4.659344   -2.047986    0.335008 >     60          1           0       -2.665316   -1.834321   -1.185671 >     61          1           0       -2.091002   -0.462021   -0.244797 >     62          1           0       -1.922516   -1.904336    1.796755 >     63          1           0       -2.544576   -3.281805    0.893097 >     64          1           0        0.507775   -2.068308    2.147908 >     65          1           0        1.781806   -4.155525   -1.297041 >     66          1           0       -0.920844   -3.679609   -1.486549 >     67          1           0        2.894807   -2.669013    2.096559 >     68          1           0        3.014140   -4.295093    1.425876 >     69          1           0        4.963853   -3.161656    0.752730 >     70          1           0        4.005879   -3.316291   -0.696652 >     71          1           0        4.239162   -0.767781    1.005710 >     72          1           0        3.230411   -0.914403   -0.422050 >     73          1           0        5.193359    0.214561   -1.108726 >     74          1           0        5.265526   -1.383240   -1.820424 >     75          1           0        6.917350   -2.097818   -0.055060 >     76          1           0        6.795441   -0.513577    0.700785 >     77          1           0        7.676786    0.560314   -1.388484 >     78          1           0        7.775572   -1.012384   -2.170056 >     79          1           0        9.765873    1.368902   -0.292993 >     80          1           0       11.930692   -2.220611    0.184757 >     81          1           0        9.425801   -2.818683   -0.806338 >     82          1           0       13.210734    0.188576    0.028579 >     83          1           0       12.495149    0.238787    1.647686 >     84          1           0       11.477000    2.287609    2.512282 >     85          1           0       11.235617    4.739753    2.323972 >     86          1           0       11.850508    5.891527    0.216208 >     87          1           0       12.718127    4.583952   -1.703277 >     88          1           0       12.964379    2.133818   -1.524213 >  --------------------------------------------------------------------- >  Rotational constants (GHZ):      0.1679224      0.0103802      0.0099533 >  Standard basis: 6-311+G(d,p) (5D, 7F) >  There are  1184 symmetry adapted basis functions of A   symmetry. >  Integral buffers will be    262144 words long. >  Raffenetti 2 integral format. >  Two-electron integral symmetry is turned on. >  1184 basis functions,  1852 primitive gaussians,  1225 cartesian basis functions >   148 alpha electrons      148 beta electrons >       nuclear repulsion energy      3740.7282424628 Hartrees. >  NAtoms=   88 NActive=   88 NUniq=   88 SFac= 7.50D-01 NAtFMM=   80 NAOKFM=T Big=T >  One-electron integrals computed using PRISM. >  NBasis=  1184 RedAO= T  NBF=  1184 >  NBsUse=  1184 1.00D-06 NBFU=  1184 >  Harris functional with IExCor=  402 diagonalized for initial guess. >  ExpMin= 4.38D-02 ExpMax= 6.29D+03 ExpMxC= 9.49D+02 IAcc=2 IRadAn=         0 AccDes= 0.00D+00 >  HarFok:  IExCor=  402 AccDes= 0.00D+00 IRadAn=         0 IDoV= 1 >  ScaDFX=  1.000000  1.000000  1.000000  1.000000 >  FoFCou: FMM=F IPFlag=           0 FMFlag=      100000 FMFlg1=        2001 >         NFxFlg=           0 DoJE=T BraDBF=F KetDBF=T FulRan=T >         Omega=  0.000000  0.000000  1.000000  0.000000  0.000000 ICntrl=     500 IOpCl=  0 >         NMat0=    1 NMatS0=    1 NMatT0=    0 NMatD0=    1 NMtDS0=    0 NMtDT0=    0 >         I1Cent=           4 NGrid=           0. >  Petite list used in FoFCou. >  Initial guess orbital symmetries: >       Occupied  (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) >       Virtual   (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) (A) >                 (A) (A) (A) (A) >  The electronic state of the initial guess is 1-A. >  Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. >  Requested convergence on MAX density matrix=1.00D-06. >  Requested convergence on             energy=1.00D-06. >  No special actions if energy rises. >  Restarting incremental Fock formation. >  SCF Done:  E(RB3LYP) =  -1690.21228532     A.U. after   28 cycles >             Convg  =    0.5107D-08             -V/T =  2.0046 >  Range of M.O.s used for correlation:     1  1184 >  NBasis=  1184 NAE=   148 NBE=   148 NFC=     0 NFV=     0 >  NROrb=   1184 NOA=   148 NOB=   148 NVA=  1036 NVB=  1036 > >  **** Warning!!: The largest alpha MO coefficient is  0.12683417D+03 > >  PrsmSu:  requested number of processors reduced to:   1 ShMem   1 Linda. >  PrsmSu:  requested number of processors reduced to:   1 ShMem   1 Linda. >  Symmetrizing basis deriv contribution to polar: >  IMax=3 JMax=2 DiffMx= 0.00D+00 >  G2DrvN: will do     4 centers at a time, making   23 passes doing MaxLOS=2. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  Calling FoFCou, ICntrl=  3107 FMM=T I1Cent=   0 AccDes= 0.00D+00. >  FoFDir/FoFCou used for L=0 through L=2. >  End of G2Drv Frequency-dependent properties file   721 does not exist. >  End of G2Drv Frequency-dependent properties file   722 does not exist. >          IDoAtm=11111111111111111111111111111111111111111111111111 >          IDoAtm=11111111111111111111111111111111111111 >          Differentiating once with respect to electric field. >                with respect to dipole field. >          Differentiating once with respect to nuclear coordinates. >          There are   267 degrees of freedom in the 1st order CPHF.  IDoFFX=5. >    267 vectors produced by pass  0 Test12= 1.53D-13 1.00D-09 XBig12= 3.87D+02 6.76D+00. >  AX will form    15 AO Fock derivatives at one time. >    267 vectors produced by pass  1 Test12= 1.53D-13 1.00D-09 XBig12= 8.56D+01 1.11D+00. >    264 vectors produced by pass  2 Test12= 1.53D-13 1.00D-09 XBig12= 5.91D-01 5.93D-02. >    264 vectors produced by pass  3 Test12= 1.53D-13 1.00D-09 XBig12= 2.23D-03 3.14D-03. >    264 vectors produced by pass  4 Test12= 1.53D-13 1.00D-09 XBig12= 4.09D-06 1.29D-04. >    264 vectors produced by pass  5 Test12= 1.53D-13 1.00D-09 XBig12= 6.15D-09 4.16D-06. >    258 vectors produced by pass  6 Test12= 1.53D-13 1.00D-09 XBig12= 1.40D-11 2.66D-07. >    236 vectors produced by pass  7 Test12= 1.53D-13 1.00D-09 XBig12= 5.06D-13 2.87D-08. >    219 vectors produced by pass  8 Test12= 1.53D-13 1.00D-09 XBig12= 2.56D-14 6.21D-09. >    199 vectors produced by pass  9 Test12= 1.53D-13 1.00D-09 XBig12= 2.12D-14 5.20D-09. >    177 vectors produced by pass 10 Test12= 1.53D-13 1.00D-09 XBig12= 2.01D-14 5.01D-09. >  Internal consistency error detected in FileIO for unit 1 I=   7 J=   0 IFail= 1. > > >  dumping /fiocom/, unit = 1 NFiles =    88 SizExt =     32768 WInBlk =       512 >                   defal = F LstWrd = -1962280960 FType=2 FMxFil=10000 > >  Number           0          0          0          0          0          0          0        501 >  Base      11258363   10315776   73707520   18034688   11021824  362994176-1962321632      23552 >  End       11720192   10317312   92399104   22244864   11023360  772379936-1962280960      24552 >  End1      11720192   10317312   92399104   22244864   11023360  772379936-1962280960      24576 >  Wr Pntr   11258363   10315776   73707520   18034688   11021824  362994176 1757205680      23552 >  Rd Pntr   11258363   10315776   73707520   18034688   11021824  362994176 1757205680      23552 >  Length      461829       1536   18691584    4210176       1536  409385760      40672       1000 > >  Number         502        503        507        508        511        514        515        516 >  Base        275968      96256      97280     284160     225280    5214208    2407936     303104 >  End         279797      96829      98033     284175     260526    5915728    5214016    2407664 >  End1        280064      97280      98304     284672     260608    5916160    5214208    2407936 >  Wr Pntr     275968      96256      97280     284160     225280    5214208    2407936     303104 >  Rd Pntr     275968      96256      97280     284160     225280    5214208    2407936     303104 >  Length        3829        573        753         15      35246     701520    2806080    2104560 > >  Number         517        518        520        521        522        523        524        526 >  Base      10208768    8103936     301568     268800   11019264   10313216   11720192   14526976 >  End       10312960   10208496     301573     268835   11021632   10315584   13122048   15928832 >  End1      10313216   10208768     302080     269312   11021824   10315776   13122048   15928832 >  Wr Pntr   10208768    8103936     301568     268800   11019264   10313216   11720192   14526976 >  Rd Pntr   10208768    8103936     301568     268800   11019264   10313216   11720192   14526976 >  Length      104192    2104560          5         35       2368       2368    1401856    1401856 > >  Number         528        530        532        534        536        538        545        547 >  Base      13122048   10317312   13825024   15928832   16630784   17332736   11025408   11026944 >  End       13823568   11018832   14526544   16630352   17332304   18034256   11025422   11029312 >  End1      13824000   11019264   14526976   16630784   17332736   18034688   11025920   11029504 >  Wr Pntr   13122048   10317312   13825024   15928832   16630784   17332736   11025408   11026944 >  Rd Pntr   13122048   10317312   13825024   15928832   16630784   17332736   11025408   11026944 >  Length      701520     701520     701520     701520     701520     701520         14       2368 > >  Number         548        551        552        559        562        563        565        569 >  Base      22946816     267264      22016      43008     260608   13824000     283648   11024896 >  End       24348672     267289      22032      43009     266545   13824592     283865   11024897 >  End1      24348672     267776      22528      43520     266752   13825024     284160   11025408 >  Wr Pntr   22946816     267264      22016      43008     260608   13824000     283648   11024896 >  Rd Pntr   22946816     267264      22016      43008     260608   13824000     283648   11024896 >  Length     1401856         25         16          1       5937        592        217          1 > >  Number         571        575        577        579        580        581        582        583 >  Base      22244864     100864     282112     266752      41472     282624     280064      43520 >  End       22946384     225207     282138     266796      42677     283248     281840      43565 >  End1      22946816     225280     282624     267264      43008     283648     282112      44032 >  Wr Pntr   22244864     100864     282112     266752      41472     282624     280064      43520 >  Rd Pntr   22244864     100864     282112     266752      41472     282624     280064      43520 >  Length      701520     124343         26         44       1205        624       1776         45 > >  Number         584        588        590        598        600        603        605        606 >  Base        284672   24348672   93810176      44032   11103744     302080     302592   11023360 >  End         285200   26453232  281116016      44034   11104647     302081     302593   11024544 >  End1        285696   26453504  281116160      44544   11104768     302592     303104   11024896 >  Wr Pntr     284672   24348672   93810176      44032   11103744     302080     302592   11023360 >  Rd Pntr     284672   24348672   93810176      44032   11103744     302080     302592   11023360 >  Length         528    2104560  187305840          2        903          1          1       1184 > >  Number         607        619        634        670        674        685        694        695 >  Base      11025920     285696   92399104     269312      98304    5916160   11029504     298496 >  End       11026512     298421   93809785     275761      98936    7318016   11031872     301252 >  End1      11026944     298496   93810176     275968      99328    7318016   11032064     301568 >  Wr Pntr   11025920     285696   92399104     269312      98304    5916160   11029504     298496 >  Rd Pntr   11025920     285696   92399104     269312      98304    5916160   11029504     298496 >  Length         592      12725    1410681       6449        632    1401856       2368       2756 > >  Number         698        742        989        991        992        993        994        995 >  Base        267776    7318016      24576      37888      37376      23040      20480      22528 >  End         268304    8103928      37076      41169      37381      23140      20510      22538 >  End1        268800    8103936      37376      41472      37888      23552      20992      23040 >  Wr Pntr     267776    7318016      24576      37888      37376      23040      20480      22528 >  Rd Pntr     267776    7318016      24576      37888      37376      23040      20480      22528 >  Length         528     785912      12500       3281          5        100         30         10 > >  Number         996        997        998        999       2999       3001       3003       3005 >  Base         21504      99328      20992      44544   11032064   28558848  281116160   69497856 >  End          21604     100571      21192      95796   11103353   69497424  322054736   71602416 >  End1         22016     100864      21504      96256   11103744   69497856  322055168   71602688 >  Wr Pntr      21504      99328      20992      44544   11032064   28558848  281116160   69497856 >  Rd Pntr      21504      99328      20992      44544   11032064   28558848  281116160   69497856 >  Length         100       1243        200      51252      71289   40938576   40938576    2104560 > >  Number        3007       3026       9994       9995       9996       9997       9998       9999 >  Base      71602688   27856896 1181765696  772379936 1757205680   11104768  322055168   26453504 >  End       73707248   28558416 1757205680 1181765696-1962321632   11258363  362993744   27856544 >  End1      73707520   28558848 1757205680 1181765696-1962321632   11258363  362994176   27856896 >  Wr Pntr   71602688   27856896 1181765696  772379936 1757205680   11104768  322055168   26453504 >  Rd Pntr   71602688   27856896 1181765696  772379936 1757205680   11104768  322055168   26453504 >  Length     2104560     701520  575439984  409385760  575439984     153595   40938576    1403040 > > >  dumping /fiocom/, unit = 2 NFiles =     7 SizExt =         0 WInBlk =       512 >                   defal = F LstWrd =     2838528 FType=2 FMxFil=10000 > >  Number           0        508        522        536        538        634        998 >  Base       2836784      20480      20695    1433744    2135264      23063      20495 >  End        2838528      20495      23063    2135264    2836784    1433744      20695 >  End1       2838528      20495      23063    2135264    2836784    1433744      20695 >  Wr Pntr    2836784      20480      20695    1433744    2135264      23063      20495 >  Rd Pntr    2836784      20480      20695    1433744    2135264      23063      20495 >  Length        1744         15       2368     701520     701520    1410681        200 > > >  dumping /fiocom/, unit = 3 NFiles =     1 SizExt =    524288 WInBlk =       512 >                   defal = T LstWrd =       67072 FType=2 FMxFil=10000 > >  Number           0 >  Base         20480 >  End          67072 >  End1         67072 >  Wr Pntr      20480 >  Rd Pntr      20480 >  Length       46592 >  Error termination in NtrErr: >  NtrErr called from FIOCnC. > > Can anybody tell me that what is the problem in my calculation and why it is coming and what is its solution? Thank you very much in advance. > With regards, > Vijay Tak>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Mon Dec 13 16:21:00 2010 From: "Paul Fleurat-Lessard Paul.Fleurat-Lessard]=[ens-lyon.fr" To: CCL Subject: CCL: Ab Initio Molecular Dynamic Message-Id: <-43377-101213050933-19392-A43uUxcmGxbtseM5yHeKIg]|[server.ccl.net> X-Original-From: Paul Fleurat-Lessard Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 13 Dec 2010 11:09:25 +0100 MIME-Version: 1.0 Sent to CCL by: Paul Fleurat-Lessard [Paul.Fleurat-Lessard]=[ens-lyon.fr] Hi, > I am interested in abinitio simulation,and I am really confused about > differences between vasp& cpmd packages. Could anybody tell me what is the > main methodology s aspects between these two software? It is better to say > that if a job which is completed with vasp ,could be done with cpmd with same > results or not?(with same plane wave cutoff and same cell characteristic in > DFT and GGA with PW91 Basis set usages.) I would say that there two main differences between VASP and CPMD. First, of course, as afar as I know (I am not a Vasp expert) VASP does only Born-Oppenheimer Molecular Dynamics whereas CPMD does both BO-MD and CP-MD. Second, VASP has been designed to treat metals and is good at this whereas Carr-Parrinello-MD is really difficult if you have a metal (or anything with a zero gap). So, if you have a metallic system, I would recommend VASP. If not, then CPMD should be fine, and faster if you use CP-MD. Another choice (beside CASTEP), is CP2K that is really fast for non metallic systems. I do not know how good it is for metallic systems as I do not use it. hope this helps, Regards, Paul. -- Fleurat-Lessard Paul, Lecturer e-mail: Paul.Fleurat-Lessard() ens-lyon.fr Laboratoire de Chimie Ecole Normale Supérieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allée d'Italie Fax: + 33 (0)4 72 72 88 60 69364 Lyon Cedex 07