From chemistry-request@server.ccl.net Wed Nov 22 03:37:50 2000 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.8.7/8.8.7) with SMTP id DAA29709 for ; Wed, 22 Nov 2000 03:37:38 -0500 Received: from iris.sipp.ac.cn (202.127.25.133) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Wed, 22 Nov 2000 16:41:21 +0800 Sender: user@ccl.net Message-ID: <3A1B84CC.BE333EA4@iris.sipp.ac.cn> Date: Wed, 22 Nov 2000 16:33:16 +0800 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: question about solvation using CHARMM Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 7bit Hi: Here is a question I need some help. I am studying a enzyme made up of 700 aa( two subunit) , and when I solvated it with water in CHARMM, I can only solvate a small part of the enzyme when using tip216. -------------------------------------------------- * EMBNet Course on Molecular Dynamics Simulation * by R. Stote, A. Dejaegere, L. Falquet, D. Kuznetsov * ! Read in Topology and Parameter files open unit 1 card read name top_all22_prot.inp read RTF card unit 1 close unit 1 open unit 1 card read name par_all22_prot.inp read PARA card unit 1 close unit 1 ! Read PSF file open unit 1 card read name x.psf read psf card unit 1 ! Read in energy minimzed coordinates open unit 1 read formatted name x.pdb read coor pdb unit 1 close unit 1 coor orie ! Read in water sphere sequence open unit 1 read formatted name tip216.crd read sequence coor unit 1 rewind unit 1 ! Generate new segment for the water sphere generate bulk noangle nodihedral ! Read water sphere coordinates read coor card unit 1 append close unit 1 open write unit 8 card name x.crd write coor unit 8 card close unit 8 set 7 15.5516 set 8 15.5516 set 9 15.5516 open read unit 15 card name cubic.img read imag unit 15 image byres xcen 0.0 ycen 0.0 zcen 0.0 sele segid buld end open unit 1 card write name x-water.psf write psf card unit 1 * solvated echestatin * close unit 1 open unit 1 card write name x-water.pdb write coor pdb unit 1 * echestatin Structure with hydrogens * close unit 1 stop ------------------------------------------------- I wish you could help me. Thanks in advance. Regards, mao xiang ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Xiang Mao | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Wed Nov 22 04:37:19 2000 Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA30174 for ; Wed, 22 Nov 2000 04:37:18 -0500 Received: from lycose.saclay.cea.fr (lycose.saclay.cea.fr [132.166.192.104]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.2.D20+Y2K) with ESMTP id KAA09958 for ; Wed, 22 Nov 2000 10:37:09 +0100 (MET) Received: from penelope.saclay.cea.fr (unverified) by lycose.saclay.cea.fr (Content Technologies SMTPRS 4.1.5) with ESMTP id for ; Wed, 22 Nov 2000 10:26:55 +0100 Received: by penelope.saclay.cea.fr with Internet Mail Service (5.5.2650.21) id ; Wed, 22 Nov 2000 10:38:40 +0100 Message-ID: From: VITORGE Pierre 094605 To: "'chemistry@ccl.net'" Subject: question: visualizing vibration from Gaussian98 Date: Wed, 22 Nov 2000 10:29:26 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Hello, I am currently using Gaussian98 on Unix workstations, entering and reading data by using a PC (Intel Windows98), typically Chem3D, I can also use a Mac. As far as i know, vibrations can be visualized with GaussView or Hypechem, unfortunately I have not got these softwares: do you know a free (or noon expensive) software that can visualize vibrations from a Gaussian98 output file? Pierre Vitorge CEA Saclay DCC/DESD/SESD UMR 8587 (Universite d'Evry-CNRS-CEA) 91191 Gif sur Yvette cedex France pierre.vitorge@cea.fr phone +33 169-08-32-65, secretary: +33 169-08-32-50, fax: +33 169-08-32-42 http://perso.club-internet.fr/vitorgen/pierre/pierre.html From chemistry-request@server.ccl.net Wed Nov 22 05:45:53 2000 Received: from cheviot2.ncl.ac.uk (root@cheviot2.ncl.ac.uk [128.240.233.16]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA30494 for ; Wed, 22 Nov 2000 05:45:52 -0500 Received: from aidan.ncl.ac.uk (nbwt@aidan.ncl.ac.uk [128.240.233.1]) by cheviot2.ncl.ac.uk (8.10.1/8.10.1) with ESMTP id eAMAjeS21623; Wed, 22 Nov 2000 10:45:40 GMT Received: from localhost (nbwt@localhost) by aidan.ncl.ac.uk (8.9.3+Sun/8.9.0) with ESMTP id KAA03127; Wed, 22 Nov 2000 10:45:40 GMT X-Authentication-Warning: aidan.ncl.ac.uk: nbwt owned process doing -bs Date: Wed, 22 Nov 2000 10:45:39 +0000 (GMT) From: "Bruce. Tattershall" X-Sender: nbwt@aidan.ncl.ac.uk To: VITORGE Pierre 094605 cc: "'chemistry@ccl.net'" Subject: Re: CCL:question: visualizing vibration from Gaussian98 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Filter-Version: 1.9 (cheviot2.ncl.ac.uk) Yes, Molden gives good visualisation of vibrations. I use it in unix, using an X-windows server on my PC. http://www.cmbi.kun.nl/~schaft/molden/molden.html Bruce Tattershall Personal Email: Bruce.Tattershall@newcastle.ac.uk Dr. B.W. Tattershall, Department of Chemistry University of Newcastle, England From chemistry-request@server.ccl.net Wed Nov 22 02:45:01 2000 Received: from mailgw.barc.ernet.in ([202.54.18.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA29504 for ; Wed, 22 Nov 2000 02:44:57 -0500 Received: from apsara.barc.ernet.in (apsara.barc.ernet.in [192.168.1.21]) by mailgw.barc.ernet.in (8.9.3/8.9.3) with ESMTP id NAA07169 for ; Wed, 22 Nov 2000 13:21:41 +0530 (IST) (envelope-from tapang@apsara.barc.ernet.in) Received: from localhost (tapang@localhost) by apsara.barc.ernet.in (8.9.3/8.9.3) with ESMTP id NAA30026 for ; Wed, 22 Nov 2000 13:20:40 +0530 Date: Wed, 22 Nov 2000 13:20:40 +0530 (IST) From: "Dr.Tapan K.Ghanty" To: chemistry@ccl.net Subject: X-Ray to Cartesian conversion Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id CAA29514 Hi All, Few months back (Feb or March 2000) from CCL list I got some summary for the conversion of X-ray fractional coordinates to cartesian coordinates (which is appended below). I tried both the programs to convert one x-ray set of data to cartesian, but the programs could not correctly convert the data set. Of course, the program written in fortran is specific for some space group, but I don't know why the another program (written in C) could not work for my molecule (it has generated some correct cartesian coordinates and some incorrect (absurd) coordinates, as verified >from the bond length and bond angle values which I have with the X-ray structure), although it worked fine for the supplied input file with the program. Also, in my following fractional coordinate file, obtained from Cambridge Crystallographic Data Center (CCDC), some of the coordinates are more than 1.0, I wonder how it is possible. To my knowledge, x-ray fractional coordinates are always less equal to 1.0 . I have following input file whose structure should be -CH2-C5H4N (a radical), that is in Pyridine molecule one H is substituted by -CH2 group. I also tried Babel, but do not know what is meant by "Free format fractional coordinates" as mentioned in Babel Readme file. I tried with the following fractional coordinate file as well as by changing the format little bit but it is giving input conversion error or something like that. Also, I have tried with the Cambridge CCDC file (clf format) directly as input, but could not get any result using Babel. X-RAY DATA to CARTESIAN ANGSTROM CONVERSION 5.033 9.900 10.598 a, b, c parametrs 64.70 82.24 87.94 alpha, beta, gamma 13 No. of atoms N1 0.8845 0.1809 0.2503 C4 0.993 0.2712 0.1233 H4 0.9185 0.3644 0.0796 C5 0.214 0.2354 1.0500 H5 0.2875 0.3048 0.9614 C6 0.3220 0.0963 1.1101 C7 1.205 0.0005 0.2443 H7 1.2721 -0.0942 0.2910 C8 0.985 0.0484 0.3076 H8 0.9056 -0.0180 0.3963 C9 0.5440 0.0441 1.0352 H9A 0.6478 0.1305 0.9652 H9B 0.6617 -0.0164 1.1024 I would highly appreciate if somebody from CCL would shed some light on this problem. Also, I would like to know what is meant by "free format fractional coordinate" as mentioned in Babel Readme file. With thanks in advance, Dr. Tapan K. Ghanty Scientific Officer Chemistry Division BARC, Mumbai 400 085, INDIA ############## appended file ################################## ----- Original Message ----- From: Scheila To: Sent: Thursday, February 24, 2000 9:02 AM Subject: CCL:X-RAY - SUMMARIZED ANSWERS >I would like to thanks all the contributions of the CClers. I'm going to >summarize the answers received. >Scheila > >___________________________________________________ >QUESTION > > >I need a help to convert some x-ray data disposed in a paper. This paper >shows the data group, the a, b and c parameters and the atomic coordinates >in the format: >x y z >C1 7866(3) 3480(6) -1818(4) >C2 7641(2) 4107(6) -2989(4) >C3 7896(2) 5715(6) -3240(4) >: >: >OMEI 9490(2) 7341(7) 3845(4) >CMEI 9845(5) 5894(15) 3795(10) >W1/2* 9230 923 2984 >W2/2* 8963 2070 3358 > > >*occupancy factor f=0.5 > > >______________________________________________________ >ANSWERS > > >1- >There is a good converter named BABEL or BABELWIN (for >windows). You can convert to many file formats. I don't know >which format you are using but what you need to know is >name of the program you used to get the result you have given >in your mail. > >You can find the program at the following site > >ftp://laue.chem.ncsu.edu/pub/X-ray/babel/ > >I hope this will help you. > >Dr Ivan Basic >Rudjer Boskovic Institute >Bijenicka 54 >HR-10001 Zagreb >CROATIA > > >2- >a very good and free program is BABEL. You can find a download site at >http://www.eyesopen.com/download/babelwin.zip or at >ftp://www.ccl.net/pub/chemistry/software/UNIX/babel/ (also win and mac and >unix) > >It handles over 50 different formats. > >Find other related chemistry software in my chemistry software list (>300 in >categories) at > >http://www.claessen.net/chemistry/soft_en.html > >Regards, > >Rolf Claessen > >3- >It doesn't appear to be in any particular format, so it's up to you to >put it into some machine readable format, like PDB > >Cambridge FDAT format has a rather complicated header, and I don't >recommend it as a starting point, unless you have access to the CCDB >programs and data. > >Since it's crystal data, the coords are probably fractional, and have an >implied decimal point in front, e.g. 7866 is really 0.7866 (fractional >coords are mostly less than 1.0). > >Rick Venable [rvenable@deimos.cber.nih.gov] > >4- >Following is a C program that will convert crystal structure coordinates to >cartesians. It expects the first line to have the a, b, c axis lengths, and >and the alpha, beta, and gamma angles. Subsequent lines are an atom label >and fractional coordinates. I'll include a sample input and output file for >comparison. > >-------- >acamox.abc -- input file >-------- > 6.0690 7.5820 7.3640 84.970 79.660 114.160 > C1 .21800 .25770 .10540 > C2 .32530 .16210 -.03000 > C3 .39920 .15780 .34360 > C4 .14350 .33540 .41450 > H10 .01900 .45500 -.14400 > H21 .29300 .18400 -.14600 > H22 .26100 .01600 .01900 > H23 .50500 .20800 -.04900 > H31 .56300 .26100 .32500 > H32 .34600 .11400 .46200 > H33 .38300 .04700 .29100 > H41 0 .33200 .41000 > H42 .12700 .28800 .53900 > H43 .23600 .47000 .38700 > N1 .22880 .22820 .28880 > N2 .10890 .36370 .06280 > O1 .08840 .36910 -.12780 >-------- >acamox.xyz -- output file >-------- >Unit cell volume = 299.2115 >C1 0.662659 1.919812 0.751155 >C2 1.431563 1.082369 -0.213801 >C3 2.387214 1.538509 2.448738 >C4 0.377954 2.859331 2.954022 >H10 -1.486982 2.960348 -1.026246 >H21 1.014250 1.083006 -1.040500 >H22 1.559471 0.135396 0.135408 >H23 2.354612 1.375188 -0.349209 >H31 3.036481 2.228242 2.316181 >H32 2.356760 1.389492 3.292541 >H33 2.563208 0.703601 2.073873 >H41 -0.488344 2.829957 2.921952 >H42 0.589466 2.693343 3.841297 >H43 0.485297 3.754710 2.758037 >N1 1.062159 1.954256 2.058194 >N2 -0.384716 2.597701 0.447557 >O1 -0.777815 2.387172 -0.910794 >-------- >abc2xyz.c >-------- >#include >#include >#include >#include > >#define MAXLINLEN 81 >#define MAXLABLEN 8 >char line [MAXLINLEN+1]; >char lab [MAXLABLEN+1]; > >/* >* prototype for utility routine >*/ >char *fgetln (char *s, int n, FILE *str); > >/* >* convert crystal structure fractional coordinates to cartesian >*/ >int main (int argc, char *argv []) { > > double a, b, c; > double alpha, beta, gamma; > double z, x [2], y [3]; > double yy; > char *tok, *sep = "\t ,"; > double degrad = M_PI / 180.0; > double vol; > >/* >* first line of input is unit cell dimensions and angles in degrees >*/ > fgetln (line, MAXLINLEN, stdin); > sscanf (line, "%lf %lf %lf %lf %lf %lf", &a, &b, &c, &alpha, &beta, >&gamma); > alpha *= degrad; > beta *= degrad; > gamma *= degrad; > >/* >* put 'a' along the z axis >*/ > z = a; > >/* >* put 'b' in the zx plane >*/ > x [0] = b * sin (gamma); > x [1] = b * cos (gamma); > >/* >* = |c| |a| cos (beta) >* = |c| |b| cos (alpha) >* from this 'c' can be determined >*/ > yy = (cos (alpha) - cos (gamma) * cos (beta)) / (sin (gamma) * sin >(beta)); > y [0] = c * sin (beta) * yy; > y [1] = c * sin (beta) * sqrt (1.0 - yy * yy); > y [2] = c * cos (beta); > >/* >* volume = (a X b) . c >* with the conventions above, (a X b) is along the y axis >*/ > vol = z * x [0] * y [1]; > printf ("Unit cell volume = %8.4lf\n", vol); > >/* >* the rest of the file is lines of atom label and fractional coordinates >*/ > while (fgetln (line, MAXLINLEN, stdin)) { > fprintf (stderr, "%s\n", line); > (void) strncpy (lab, strtok (line, sep), MAXLABLEN); > tok = strtok (0, sep); a = atof (tok); > tok = strtok (0, sep); b = atof (tok); > tok = strtok (0, sep); c = atof (tok); > a = a * z + b * x [1] + c * y [2]; > b = b * x [0] + c * y [0]; > c = c * y [1]; > printf ("%-8s %11.6lf %11.6lf %11.6lf\n", lab, a, b, c); > } > > return 0; > } > >/* >* fgetln >* like fgets but always reads a full line >* newline character is never returned in s >*/ >char *fgetln (char *s, int n, FILE *str) { > > int ch, nc; > > nc = 0; > ch = getc (str); > while ((ch != EOF) && (ch != '\n') && (nc < n-1)) { > s [nc++] = (char) ch; > ch = getc (str); > } > s [nc] = 0; > >/* >* if EOF and no characters read, return null >*/ > if ((ch == EOF) && (nc == 0)) s = 0; > >/* >* if a newline hasn't been read, keep reading >*/ > while ((ch != EOF) && (ch != '\n')) { > ch = getc (str); > } > > return s; > } >-------- >Dave Heisterberg > >5- >I dont know if this helps. it depends on what software you have at >your disposal. I've solved the same problem by writing a small >spreadsheet program to convert from crystalographic coordinates >to x,y,z's. Unfortunatly the one I built was specific to the molecule >I was working on but it should be pretty trivial, its just a matrix >multiplication. The I used Gaussian's newzmat to convert this file >to pdf which spartan could then read. >I dont know if this helps >Larry Cuffe > >6- >A FORTRAN PROGRAM > >C program convert > >C This program is able to convert fractional X-Ray coordinates >C to cartesian orthonormal coordinates > > >C Eduardo Lemos de Sa > > REAL*8 AA, BB, CC, FACTOR, ALPHA, BETHA, GAMMA > REAL*8 XX, YY, ZZ, XXCART, YYCART, ZZCART > REAL*8 PI > INTEGER NCOUNT > CHARACTER TITLE*80, ATOM*5 >C >C FACTOR IS THE NUMBER THAT SHOULD MULTIPLIED THE FRACTIONAL COORDINATE > > READ(5,10) TITLE > 10 FORMAT(A80) > READ(5,*) AA, BB, CC, FACTOR > 20 FORMAT(4(D14.7)) > READ(5,*) ALPHA, BETHA, GAMMA > 30 FORMAT(3(F10.3)) > READ(5,*) NCOUNT > 40 FORMAT(I4) > >C SETS THE PI (3.141592..) VALUE > PI=4*ATAN(1.0D0) >C >C CONVERT THE ANGLE (DEG - > RADIAN) > > ALPHA=ALPHA*PI/180.0D0 > BETHA=BETHA*PI/180.0D0 > GAMMA=GAMMA*PI/180.0D0 > > WRITE(6,40) NCOUNT > WRITE(6,10) TITLE >C > 150 FORMAT(A2, 3F10.5) >C BEGINS THE READ DATA INPUT (TITLE) > > DO 100 J=1,NCOUNT > > READ(5,150) ATOM, XX, YY, ZZ > XX=XX*AA*FACTOR > YY=YY*BB*FACTOR > ZZ=ZZ*CC*FACTOR > XXCART=XX+YY*COS(GAMMA)+ZZ*COS(BETHA) > YYCART=YY*SIN(GAMMA)-ZZ*SIN(BETHA)*COS(ALPHA) > ZZCART=ZZ*SIN(BETHA)*SIN(ALPHA) > WRITE(6,150) ATOM, XXCART, YYCART, ZZCART > > 100 CONTINUE > > STOP > END > > > > > INPUT MODEL >Dados provenientes do raios-X de Giovana - dimero Ti >10.8611 10.5932 15.3648 1.000D-4 >90.000 102.826 90.000 >4 >ti 1139.0 967.0 346.0 >cl 3057.0 546.0 1406.0 >o 388.0 -794.0 596.0 >o 304.0 1635.0 1170.0 > > >OUTPUT MODEL > 4 >Dados provenientes do raios-X de Giovana - dimero Ti >ti 1.11906 1.02436 .51836 >cl 2.84067 .57839 2.10639 >o .21812 -.84110 .89289 >o -.06889 1.73199 1.75283 > > >EDUARDO LEMOS DE SÁ > > > ************************************************************************ Dr. Tapan K. Ghanty Theoretical Chemistry Section Chemistry Division Bhabha Atomic Research Centre Trombay, Mumbai 400 085 India Phone: 550 5050, 550 5010, 550 5000, 556 3120 Extn. 2675 ----------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Nov 21 19:51:44 2000 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.8.7/8.8.7) with SMTP id TAA27888 for ; Tue, 21 Nov 2000 19:51:22 -0500 Received: from iris.sipp.ac.cn (202.127.25.133) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Wed, 22 Nov 2000 08:53:01 +0800 Sender: user@ccl.net Message-ID: <3A1B1718.9EA73FB@iris.sipp.ac.cn> Date: Wed, 22 Nov 2000 08:45:12 +0800 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: more summary about adding hydrogen Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 7bit Hi: Here is another two email replying my questoin that I forgot to put them in my last eamil. Thanks. ---------------- From: Deepak Singh Hi YOu should theoretically not need to use HBUILD. Just use IC PARAM IC BUILD where you used HBUILD. From: emad@ks.uiuc.edu> I am not an expert, either. However, I could solve this problem by addition of the sgment name to the lines of coordinate. For example you are generating "PROT" segment. In this case, I think CHARMM tries to find the corresponding coordinate for the atom, the residue, and the segment as specified in psf file. If you look at the first error, there is nothing for segname: ** WARNING ** For atom in coordinate file, could not find residue in PSF, and is thus ignored: SEGID= RESID=1 RESNAME= GLU TYPE= N *** LEVEL 1 WARNING *** BOMLEV IS 0 I edited the pdb file and added the segname at the end of the coordinate lines. Then it worked. The format is fixed. Use the following line as an example (If the line is broken to two line, it is because of my editor, join them first): ATOM 1 N ALA A 19 158.405 67.834 38.687 1.00101.61 PROT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Xiang Mao | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Wed Nov 22 04:53:07 2000 Received: from quim.iq.usp.br (quim.iq.usp.br [143.107.46.101]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA30261 for ; Wed, 22 Nov 2000 04:53:03 -0500 Received: (from sjardino@localhost) by quim.iq.usp.br (8.9.3/8.9.3) id HAA14140; Wed, 22 Nov 2000 07:51:05 -0200 (EDT) Date: Wed, 22 Nov 2000 07:51:05 -0200 (EDT) From: Sergio Augusto Jardino Filho To: chemistry@ccl.net Subject: CAGE COMPOUNDS Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Colleages, I study cage compounds with computational methods, and I wonder the meaning of the expression "differential correlation energy" I read in the article: Accurate quantum chemical calculation of the relative energetics of C20 carbon clusters via localized multireference perturbation calculations Murphy, R. B.; Friesner, R. A. Chem. Phys. Lett. 288 (1998) 403-407. This term is important to understand the effect of the basis set in the structure, and as I have never seen that before, I ask your help. Thanks in advance Sergio Augusto Jardino Filho Instituto de Quimica Universidade de Sao Paulo Brazil From chemistry-request@server.ccl.net Wed Nov 22 05:39:33 2000 Received: from mailhub.usp.br (serv1.uspnet.usp.br [143.107.253.61]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA30462 for ; Wed, 22 Nov 2000 05:39:27 -0500 Received: (qmail 23239 invoked from network); 22 Nov 2000 10:39:10 -0000 Received: from unknown (HELO sergio) (143.107.194.151) by mailhub.usp.br with SMTP; 22 Nov 2000 10:39:10 -0000 Message-ID: <001101c05470$29d3f180$97c26b8f@ligquim.ffclrp.usp.br> Reply-To: =?iso-8859-1?Q?S=E9rgio_Emanuel_Galembeck?= From: =?iso-8859-1?Q?S=E9rgio_Emanuel_Galembeck?= To: "VITORGE Pierre 094605" , References: Subject: Re: CCL:question: visualizing vibration from Gaussian98 Date: Wed, 22 Nov 2000 08:37:05 -0200 Organization: =?iso-8859-1?Q?Universidade_de_S=E3o_Paulo?= MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Pierre, A good software for visualization of molecular vibrations is Molden. Yiu will find it in: http://www.caos.kun.nl/~schaft/molden/molden.html Hope this help you Sergio Galembeck ----- Original Message ----- From: "VITORGE Pierre 094605" To: Sent: Wednesday, November 22, 2000 7:29 AM Subject: CCL:question: visualizing vibration from Gaussian98 > Hello, > > I am currently using Gaussian98 on Unix workstations, entering and reading > data by using a PC (Intel Windows98), typically Chem3D, I can also use a > Mac. > As far as i know, vibrations can be visualized with GaussView or Hypechem, > unfortunately I have not got these softwares: do you know a free (or noon > expensive) software that can visualize vibrations from a Gaussian98 output > file? > > Pierre Vitorge > CEA Saclay > DCC/DESD/SESD > UMR 8587 (Universite d'Evry-CNRS-CEA) > 91191 Gif sur Yvette cedex > France > > pierre.vitorge@cea.fr > phone +33 169-08-32-65, > secretary: +33 169-08-32-50, > fax: +33 169-08-32-42 > > http://perso.club-internet.fr/vitorgen/pierre/pierre.html > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Tue Nov 21 22:04:29 2000 Received: from mailcity.com (fes-qout.whowhere.com [209.185.123.96]) by server.ccl.net (8.8.7/8.8.7) with SMTP id WAA28546 for ; Tue, 21 Nov 2000 22:04:29 -0500 Received: from Unknown/Local ([?.?.?.?]) by mailcity.com; Tue Nov 21 18:54:39 2000 To: amber@cgl.ucsf.edu Date: Tue, 21 Nov 2000 21:54:39 -0500 From: "Sam Andersen" Message-ID: Mime-Version: 1.0 Cc: chemistry@ccl.net X-Sent-Mail: on Reply-To: sam_ccl@lycos.com X-Mailer: MailCity Service Subject: Performance of Compaq ES vs IBM or ORIGIN servers X-Sender-Ip: 209.42.199.82 Organization: Lycos Communications (http://comm.lycos.com:80) Content-Type: text/plain; charset=us-ascii Content-Language: en Content-Transfer-Encoding: 7bit Hi, Does anybody have Compaq/DEC multiprocessor ALPHA servers that are being used for MD simulations by AMBER or CHARMM using MPI or any other parallel arch.? We are planning to buy 4 or 8 processor ES40 or GS60 DEC server. This is for dedicated parallel processing on all processors for MD simulations of large protein systems (sizes of about 100K atoms). We have been using SGI-ORIGIN series of machines for MD simulations and have NO experience with compaq systems (for parallel jobs). Are there people in chemistry community using these servers (under Tru64 UNIX and MPI/OPEMMP) for MD or other apps?. I would appreciate if somebody comment on their efficeincy in parallel jobs (particulalry SANDER or GIBBS of AMBER6). Also, if people out there use other systems like multiprocessor SGI-ORIGIN or IBM-SP2, Could you please comment on relative performance of parallel execution of AMBER codes on these systems? If people have expereinced particular probelms in running parallel jobs (particularly AMBER6 MD simulations)on multiprocessor ES40 or GS60 compaq/DEC systems, Please share your experience. I will post summary. Thanks and happy thanksgiving weekend. Sam Get FREE Email/Voicemail with 15MB at Lycos Communications at http://comm.lycos.com From chemistry-request@server.ccl.net Wed Nov 22 08:54:54 2000 Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA32715 for ; Wed, 22 Nov 2000 08:54:52 -0500 Received: from gotham.ccc.nottingham.ac.uk ([128.243.40.48] helo=unix.ccc.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.16 #1) id 13yaLT-0002LU-00 for chemistry@ccl.net; Wed, 22 Nov 2000 13:53:55 +0000 Received: from granby ([128.243.40.43] helo=granby.ccc.nottingham.ac.uk) by unix.ccc.nottingham.ac.uk with esmtp (Exim 3.16 #1) id 13yaM8-0005df-00 for chemistry@ccl.net; Wed, 22 Nov 2000 13:54:36 +0000 Date: Wed, 22 Nov 2000 13:54:35 +0000 (GMT) From: Simon Cross X-Sender: pcxsc@granby.ccc.nottingham.ac.uk To: ccl list Subject: Amber5 RESP Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I'm trying to parameterise partial charges for a phosphonate for use in Amber5. I have used Gaussian98 to calculate the dihedral torsion barriers for 3 crucial bonds and also have a globally optimised structure. These have been optimised using #HF/3-21G* within Gaussian98. For parameterisation of the charges within Gaussian however, the Amber web page seems to use HF 6-31G*, but the readme file within the software seems to imply using the mp2 6-31G* basis set to get the ESP charges. Can anyone tell me which is correct to use? Cheers, ----------------------------------------- Simon Cross School of Chemistry University of Nottingham tel. 0115 9514193 Email: pcxsc@nottingham.ac.uk From chemistry-request@server.ccl.net Wed Nov 22 10:46:53 2000 Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA00559 for ; Wed, 22 Nov 2000 10:46:37 -0500 Received: from localhost (fgonzale@localhost) by lauca.usach.cl (8.10.0.Beta12/8.10.0.Beta10) with ESMTP id eAMFhTl19873 for ; Wed, 22 Nov 2000 12:43:29 -0300 (CDT) Date: Wed, 22 Nov 2000 12:43:29 -0300 (CDT) From: Fdo Danilo Gonzalez Nilo To: chemistry@ccl.net Subject: INDO param Hyperchem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all! Anybody know how can I change the INDO parameters in Hyperchem? Thanks a lot! Danilo/// From chemistry-request@server.ccl.net Wed Nov 22 11:05:00 2000 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA00647 for ; Wed, 22 Nov 2000 11:04:49 -0500 Received: from olymp.cup.uni-muenchen.de by mailrelay2.lrz-muenchen.de for CHEMISTRY@ccl.net; Wed, 22 Nov 2000 17:04:31 +0100 Received: by olymp.cup.uni-muenchen.de (AIX 3.2/UCB 5.64/4.03) id AA28312; Wed, 22 Nov 2000 17:04:28 +0100 Date: Wed, 22 Nov 2000 17:04:27 +0100 (MET) From: Stefan Seidler To: CHEMISTRY@ccl.net Subject: CCL:X-Ray to Cartesian conversion Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Tapan, the header for the babel "Free format fractional coordinates" is as follows (from babel file rdfract.c function read_fform_fract()): no_atoms alpha beta gamma a b c empty_line atomsymb fx fy fz ... The conversion from fractional to cartesian coordinates is perfect, but to get one connected molecule as you may expect you need to adjust the fractional coordinates. To take into account the translational periodicity add and subtract multiples of 1 to the x y and z fractional coordinates. The easiest way is to automatically build a "crystal" by a programm (CRYSIN command in Sybyl or Solids_Builder in InsighII) and extract a single complete structure. A set of cartesian coordinates for your -CH2-C5H4N are: N1 4.8742 2.9112 2.3771 C4 5.2707 3.2356 1.1710 H4 4.8664 3.9619 0.7560 C7 6.4145 1.0996 2.3201 H7 6.7854 0.3719 2.7636 C8 5.4149 1.8571 2.9213 H8 5.1186 1.5976 3.7637 C5 6.2654 2.5530 0.4749 H5 6.5332 2.8426 -0.3666 C6 6.8454 1.4461 1.0456 C9 7.8370 0.5940 0.3343 H9A 8.2900 1.1352 -0.3305 H9B 8.5040 0.2966 0.9725 Hope this helps, Stefan mailto:Stefan.Seidler@cup.uni-muenchen.de From chemistry-request@server.ccl.net Wed Nov 22 07:19:43 2000 Received: from quim.iq.usp.br (quim.iq.usp.br [143.107.46.101]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA32108 for ; Wed, 22 Nov 2000 07:19:39 -0500 Received: (from sjardino@localhost) by quim.iq.usp.br (8.9.3/8.9.3) id KAA18036; Wed, 22 Nov 2000 10:17:34 -0200 (EDT) Date: Wed, 22 Nov 2000 10:17:34 -0200 (EDT) From: Sergio Augusto Jardino Filho To: chemistry@ccl.net Subject: Bond order Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id HAA32110 Dear Colleages, I wonder how to calculate bond order from a set of eigenvalues of energies of MO? Could anyone help me? Sergio A. Jardino Fº Instituto de Quimica Universidade de Sao Paulo Brazil From chemistry-request@server.ccl.net Wed Nov 22 07:12:18 2000 Received: from mum.mans.eun.eg (mum.mans.eun.eg [193.227.50.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA32068 for ; Wed, 22 Nov 2000 07:12:15 -0500 Received: by mum.mans.eun.eg with Internet Mail Service (5.5.2650.21) id ; Wed, 22 Nov 2000 14:14:25 +0200 Message-ID: <4EF2E03A9B67D2119E2E0000F8053499427497@mum.mans.eun.eg> From: Tarek Mamoun El-Gogary To: "'CHEMISTRY@ccl.net'" Subject: experimental force constants Date: Wed, 22 Nov 2000 14:14:24 +0200 Dear members, I wonder if some one could help me getting the experimental force constants for the different internal coordinates of tetrahydro pyrrole molecule. Regards Tarek From chemistry-request@server.ccl.net Wed Nov 22 09:40:57 2000 Received: from silver.ch.unito.it (silver.ch.unito.it [130.192.118.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA00265 for ; Wed, 22 Nov 2000 09:40:56 -0500 Received: from chpc47.ch.unito.it (chpc47.ch.unito.it [130.192.118.47]) by silver.ch.unito.it (8.9.3/8.9.3) with SMTP id PAA23463 for ; Wed, 22 Nov 2000 15:56:25 +0100 (MET) Message-Id: <3.0.3.32.20001122153859.007c3430@silver.ch.unito.it> X-Sender: teorica@silver.ch.unito.it (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Wed, 22 Nov 2000 15:38:59 +0100 To: chemistry@ccl.net From: Theoretical Chemistry Group Subject: Re: CCL:question: visualizing vibration from Gaussian98 In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" A free software running on Windows PC is MOLDRAW. It reads GAUSSIAN output file (and many other formats) visualizing vibrations. http://www.ch.unito.it/ifm/fisica/moldraw/moldraw.html Theoretical Chemistry Group University of Torino From chemistry-request@server.ccl.net Wed Nov 22 14:03:06 2000 Received: from sunflare.ccs.yorku.ca (sunflare.ccs.yorku.ca [130.63.236.128]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA01473 for ; Wed, 22 Nov 2000 14:03:06 -0500 Received: from sunlight.ccs.yorku.ca (sunlight.ccs.yorku.ca [130.63.236.85]) by sunflare.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id OAA15241; Wed, 22 Nov 2000 14:02:45 -0500 (EST) Received: from localhost (serge@localhost) by sunlight.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id OAA16829; Wed, 22 Nov 2000 14:02:34 -0500 (EST) X-Authentication-Warning: sunlight.ccs.yorku.ca: serge owned process doing -bs Date: Wed, 22 Nov 2000 14:02:34 -0500 (EST) From: "S.I.Gorelsky" X-Sender: To: Fdo Danilo Gonzalez Nilo cc: Subject: INDO param Hyperchem In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Hi all! > Anybody know how can I change the INDO parameters in Hyperchem? > Thanks a lot! > Danilo/// You can modify parameters used for semiempirical methods in HyperChem by changing the corresponding *.abp files. They are located in the subdirectory RUNFILES. Please also refer to the HyperChem manual ("Reference"), Appendix C. CNDO and INDO parameter file is cindo.abp ZINDO/1 parameter files are zindo1_1.abp, zindo1_2.abp, and zindo1_3.abp ZINDO/S parameter files are zindos_1.abp, zindos_2.abp, zindos_3.abp, and zindos_4.abp Good luck! ________________________________________________________________ Sergey Gorelsky, M. Sc. Department of Chemistry, York University 4700 Keele Street, Toronto, Ontario M3J 1P3 tel.(416) 736-2100 ext#77720 and ext#70131 fax:(416) 736-5936 http://www.chem.yorku.ca/grad/SG/ ________________________________________________________________ From chemistry-request@server.ccl.net Wed Nov 22 22:32:39 2000 Received: from mx1-gbe1.aist.go.jp (mx1.aist.go.jp [150.29.246.133]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id WAA03380 for ; Wed, 22 Nov 2000 22:32:38 -0500 Received: from mx1.aist.go.jp by mx1-gbe1.aist.go.jp (8.9.3+Sun/aist) with SMTP id MAA16528 for ; Thu, 23 Nov 2000 12:32:31 +0900 (JST) Received: (qmail 16525 invoked from network); 23 Nov 2000 12:32:31 +0900 Received: from tnhost2.tniri.go.jp (150.82.50.245) by mx1.aist.go.jp with SMTP; 23 Nov 2000 12:32:31 +0900 Received: from tniri.go.jp ([150.82.48.227]) by tnhost2.tniri.go.jp (8.9.3/3.7W) with ESMTP id MAA18427 for ; Thu, 23 Nov 2000 12:32:31 +0900 (JST) Message-ID: <3A1C9005.3624F582@tniri.go.jp> Date: Thu, 23 Nov 2000 12:33:25 +0900 From: Abhijit Chatterjee X-Mailer: Mozilla 4.73 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Thermal energy Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Friends, I wish to calculate Thermal energy and entropy using DFT. How one can calculate the parameters using DFT? Looking forward to your comments and suggestions. I will post the summary. Cheers ABhijit Chatterjee email: chatt@tniri.go.jp