From chemistry-request@ccl.net Mon Jun 28 03:03:42 2004 Received: from mail3.cc.huji.ac.il (real-outmail.cc.huji.ac.il [132.64.1.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5S83fkJ006495 for ; Mon, 28 Jun 2004 03:03:42 -0500 Received: by mail3.cc.huji.ac.il (Postfix, from userid 31998) id 384C368040; Mon, 28 Jun 2004 11:08:48 +0300 (IDT) Received: from devesh (xstat1.ch.huji.ac.il [132.64.98.56]) by mail3.cc.huji.ac.il (Postfix) with SMTP id 0BF9968055 for ; Mon, 28 Jun 2004 11:08:48 +0300 (IDT) Message-ID: <004601c45d08$90d75850$801da8c0@devesh> From: "Dr. Devesh Kumar" To: Subject: Input to calculate g tensor Date: Mon, 28 Jun 2004 13:08:04 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0043_01C45D10.F2780BB0" X-Priority: 3 X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Level: This is a multi-part message in MIME format. ------=_NextPart_000_0043_01C45D10.F2780BB0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, Can any body suggest me what are the keywords to get g-tensor using = Gaussian 03? Thanks Devesh ------=_NextPart_000_0043_01C45D10.F2780BB0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi,

Can any body suggest me what are the = keywords to=20 get g-tensor using Gaussian 03?

Thanks

Devesh

------=_NextPart_000_0043_01C45D10.F2780BB0-- From chemistry-request@ccl.net Mon Jun 28 04:15:30 2004 Received: from pc15190.chemie.uni-marburg.de (pc15190.Chemie.Uni-Marburg.DE [137.248.152.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5S9FTAO010359 for ; Mon, 28 Jun 2004 04:15:29 -0500 Received: from sg1503.chemie.uni-marburg.de (root|at|sg1503.Chemie.Uni-Marburg.DE [137.248.151.215]) by pc15190.chemie.uni-marburg.de (8.12.11/8.12.9/schn) with ESMTP id i5S9KN04003894 for ; Mon, 28 Jun 2004 11:20:25 +0200 Received: from lein.chemie.uni-marburg.de (pc15217.Chemie.Uni-Marburg.DE [137.248.152.51]) by sg1503.chemie.uni-marburg.de (8.12.10/8.12.10/schn) with ESMTP id i5S9KLG7012124 for ; Mon, 28 Jun 2004 09:20:22 GMT Received: from lein.chemie.uni-marburg.de (localhost [127.0.0.1]) by lein.chemie.uni-marburg.de (8.12.3/8.12.3/SuSE Linux 0.6) with ESMTP id i5S9HYH8012164 for ; Mon, 28 Jun 2004 11:17:34 +0200 Received: (from matthias@localhost) by lein.chemie.uni-marburg.de (8.12.3/8.12.3/Submit) id i5S9HYDL012163 for chemistry|at|ccl.net; Mon, 28 Jun 2004 11:17:34 +0200 Date: Mon, 28 Jun 2004 11:17:34 +0200 From: Matthias Lein To: CCL-List Subject: Hindered Rotor Analysis in G03 Message-ID: <20040628091734.GA12140|at|chemie.uni-marburg.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline User-Agent: Mutt/1.4.1i X-Spam-Status: No, hits=0.9 required=7.5 tests=MY_BAD_DOT autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net X-Virus-Scanned: by amavisd-new Hi all, investigating a molecule of 72 atoms I calculated the thermodynamical data of dissociation given by standard frequency analysis of Gaussian98 (and G03). Given one rotational barrier of about 10 kcal/mol I thought it to be useful to try the "Freq(HinderedRotor)"-Keyword in Gaussian to correct the data for contributions of internal rotation. I used an already finished harmonic frequency analysis and the "readfc"-keyword to avoid recalculation of the frequencies. The algorithm of Schlegel et al. found two internal rotations but then skipped the calculation with the following lines: > Check for ring deformation > Number of internal rotation degrees of freedom = 2 > NNew= 156 NTest= 2 NB= 45 IFrz= 0 IBar= 7 ICyc= 0 > Problem with the number of degrees of freedom > Error termination via Link716 My questions: 1) Does anyone know the limitations of this keyword? (No of atoms, degrees of freedom,...) 2) Is there knowledge about problems and performance of this method, including numerical values (is it necessary or reasonable to use these corrections)? Thanks in advance Matthias. From chemistry-request@ccl.net Sun Jun 27 20:42:02 2004 Received: from web15208.mail.bjs.yahoo.com (web15208.mail.cnb.yahoo.com [202.43.216.138]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i5S1ftkJ027733 for ; Sun, 27 Jun 2004 20:41:56 -0500 Message-ID: <20040628014701.1456.qmail_at_web15208.mail.bjs.yahoo.com> Received: from [202.201.245.108] by web15208.mail.cnb.yahoo.com via HTTP; Mon, 28 Jun 2004 09:47:01 CST Date: Mon, 28 Jun 2004 09:47:01 +0800 (CST) From: =?gb2312?q?yong=20guo?= Subject: CCL:consultation To: chemistry_at_ccl.net Content-Transfer-Encoding: 8bit Dear sir: I want to research the property of molecule in solvent . by reaserch the literature in J.C.P , J.P.C and J.Mol.Struc (Theo), i find PCM solvent model is most popular, IPCM and SCIPCM is lesser and in recent year,Onsager model is rare seen therefore i decide to study the property of molecule with PCM solven model. however if i want to compare the result of PCM model with the result in another solvent model , what solvent model i should to choose ? the molelule i want to study is organics containing C,H, N, O, Br and S.the purpose is to study the solvent molecule' influence on the molecule conformation. I has cultivated two crystals in same solvent: in one crystal, a intermolecular hydrogen bond formed between molecule of title compound and solvent molecule; in another crystal, no solvent molecule existed. the conformation of two molecule of title compound is different. I want to research the interesting phenomenon and to explain the difference between their structure by comparing the two molecular energy,charge and orbit in solution. in addition, i has maked a OPT+FREQ calculation in PCM model.the OPT calculation is finished normally,but the Freq calculation is not.i try to increase the space of RWF,but it fail again. the following is my input file and error information: input file: %chk=B3LYP3-21(d)freq %mem=95MW %rwf=1,2gb,2,2gb,3,3gb,4,4gb %nproc=1 Will use up to 1 processors via shared memory. Default route: MaxDisk=6000MB -------------------------------------------------------------- # freq rb3lyp/3-21g* scrf=(solvent=methanol) geom=connectivity -------------------------------------------------------------- 1/10=4,30=1,38=1,57=2/1,3; 2/17=6,18=5,40=1/2; 3/5=5,7=1,11=2,16=1,25=1,30=1,70=2201,71=2,72=3,74=-5/1,2,3; 4/7=1/1; 5/5=2,38=5,53=3/2; 8/6=4,10=90,11=11,27=1476395008/1; 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; ---------------------------------------------------------------- 1482-confromation before rotation in methanol,B3LYP/3-21(d,)freq ---------------------------------------------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 Br S 1 B1 O 2 B2 1 A1 N 3 B3 2 A2 1 D1 0 N 4 B4 3 A3 2 D2 0 N 3 B5 2 A4 1 D3 0 N 6 B6 3 A5 2 D4 0 N 7 B7 6 A6 3 D5 0 C 4 B8 3 A7 2 D6 0 C 9 B9 4 A8 3 D7 0 C 10 B10 9 A9 4 D8 0 C 11 B11 10 A10 9 D9 0 C 12 B12 11 A11 10 D10 0 C 13 B13 12 A12 11 D11 0 C 3 B14 2 A13 1 D12 0 C 15 B15 3 A14 2 D13 0 C 5 B16 4 A15 3 D14 0 C 17 B17 5 A16 4 D15 0 C 6 B18 3 A17 2 D16 0 C 19 B19 6 A18 3 D17 0 C 20 B20 19 A19 6 D18 0 C 21 B21 20 A20 19 D19 0 C 22 B22 21 A21 20 D20 0 C 23 B23 22 A22 21 D21 0 C 24 B24 23 A23 22 D22 0 C 8 B25 7 A24 6 D23 0 H 9 B26 4 A25 3 D24 0 H 10 B27 9 A26 4 D25 0 H 11 B28 10 A27 9 D26 0 H 12 B29 11 A28 10 D27 0 H 13 B30 12 A29 11 D28 0 H 18 B31 17 A30 5 D29 0 H 18 B32 17 A31 5 D30 0 H 18 B33 17 A32 5 D31 0 H 21 B34 20 A33 19 D32 0 H 22 B35 21 A34 20 D33 0 H 24 B36 23 A35 22 D34 0 H 25 B37 24 A36 23 D35 0 H 5 B38 4 A37 3 D36 0 H 7 B39 6 A38 3 D37 0 H 8 B40 7 A39 6 D38 0 H 8 B41 7 A40 6 D39 0 Variables: B1 10.67373 B2 4.16402 B3 2.3481 B4 1.41276 B5 3.30826 B6 1.41548 B7 2.30254 B8 2.44331 B9 1.39434 B10 1.39793 B11 1.39707 B12 1.39514 B13 1.40231 B14 1.26511 B15 1.45225 B16 1.35573 B17 1.49804 B18 1.30458 B19 1.49572 B20 1.40447 B21 1.39554 B22 1.39533 B23 1.39608 B24 1.39438 B25 1.33757 B26 1.07936 B27 1.08625 B28 1.08572 B29 1.08615 B30 1.08524 B31 1.09499 B32 1.09127 B33 1.09508 B34 1.08598 B35 1.08497 B36 1.08512 B37 1.08463 B38 1.03448 B39 1.04485 B40 1.01993 B41 1.01995 A1 57.09252 A2 142.51866 A3 135.07039 A4 62.80545 A5 51.2932 A6 85.95196 A7 75.20783 A8 149.82307 A9 120.79443 A10 119.39451 A11 120.47025 A12 119.89068 A13 126.41181 A14 131.20948 A15 109.09001 A16 119.96533 A17 72.41396 A18 113.80042 A19 120.4459 A20 120.59159 A21 119.28068 A22 121.10187 A23 119.19826 A24 31.88919 A25 88.98099 A26 119.05743 A27 120.34044 A28 120.30675 A29 119.60116 A30 110.35367 A31 110.26277 A32 110.47538 A33 119.84086 A34 120.40912 A35 120.30978 A36 119.8184 A37 119.38078 A38 119.22487 A39 152.32008 A40 86.93087 D1 83.47137 D2 -70.60541 D3 5.63703 D4 8.17439 D5 -165.34043 D6 105.17907 D7 158.24491 D8 -0.1314 D9 -0.81595 D10 0.18905 D11 0.97037 D12 46.85752 D13 -45.47392 D14 0.36709 D15 174.43697 D16 164.82395 D17 157.55167 D18 -135.01991 D19 177.32056 D20 0.03591 D21 -0.59472 D22 0.10169 D23 174.67873 D24 -20.79312 D25 179.64803 D26 179.64874 D27 -179.03952 D28 -177.94265 D29 -24.08897 D30 -144.76154 D31 96.08981 D32 -1.97757 D33 -179.56041 D34 179.92336 D35 179.89915 D36 157.58462 D37 -0.50577 D38 175.80171 D39 -2.30846 error information: NSum of APT charges= 0.35270 APT Atomic charges with hydrogens summed into heavy atoms: 1 1 Br -0.348376 2 S -1.146245 3 O -1.027842 4 N -0.834813 5 N -0.186505 6 N -0.150731 7 N -0.852982 8 N -0.259442 9 C -0.033129 10 C 0.118845 11 C -0.036959 12 C 0.089505 13 C -0.082063 14 C 0.686961 15 C 1.204521 16 C -0.788394 17 C 0.826498 18 C 0.065219 19 C 0.718120 20 C -0.076351 21 C 0.050490 22 C -0.102428 23 C 0.519564 24 C -0.086937 25 C 0.060537 26 C 2.025635 27 H 0.000000 28 H 0.000000 29 H 0.000000 30 H 0.000000 31 H 0.000000 32 H 0.000000 33 H 0.000000 34 H 0.000000 35 H 0.000000 36 H 0.000000 37 H 0.000000 38 H 0.000000 39 H 0.000000 40 H 0.000000 41 H 0.000000 42 H 0.000000 Sum of APT charges= 0.35270 Electronic spatial extent (au): = 16756.0205 Charge= 0.0000 electrons Dipole moment (field-independent basis, Debye): X= 4.4781 Y= -13.9645 Z= 5.1624 Tot= 15.5471 Quadrupole moment (field-independent basis, Debye-Ang): XX= -171.9310 YY= -177.5606 ZZ= -168.0004 XY= 55.2926 XZ= -0.8687 YZ= -2.9272 Traceless Quadrupole moment (field-independent basis, Debye-Ang): XX= 0.5663 YY= -5.0633 ZZ= 4.4969 XY= 55.2926 XZ= -0.8687 YZ= -2.9272 Octapole moment (field-independent basis, Debye-Ang**2): XXX= 76.3040 YYY= -260.9683 ZZZ= 10.1579 XYY= 192.9949 XXY= -153.3713 XXZ= -6.1382 XZZ= 78.1987 YZZ= -36.9377 YYZ= 32.8431 XYZ= 22.2143 Hexadecapole moment (field-independent basis, Debye-Ang**3): XXXX=-12680.0968 YYYY= -6426.2374 ZZZZ= -584.3541 XXXY= 456.0998 XXXZ= 240.0490 YYYX= 1028.6885 YYYZ= 5.0575 ZZZX= -109.8996 ZZZY= -36.8108 XXYY= -3348.7631 XXZZ= -2487.6433 YYZZ= -1137.9718 XXYZ= 94.1140 YYXZ= -65.0780 ZZXY= -70.7703 N-N= 2.709998116592D+03 E-N=-1.489621355248D+04 KE= 3.981653343482D+03 Exact polarizability: 490.904 -43.677 431.547 42.754 -2.982 143.667 Approx polarizability: 521.672 -44.663 496.046 54.897 -8.847 176.906 D1PCM: PCM CHGder 1st derivatives, ID1Alg=0 FixD1E=F DoIter=F I1PDM=0. D2PCM: PCM 2nd derivatives, FixD2E=F I1PDM=0. D2PCM-2 allocation failure: iend,mxcore= 119167574 99361975 Error termination via Lnk1e in e:\g03w\l701.exe at Mon Jun 28 05:48:45 2004. Job cpu time: 0 days 6 hours 5 minutes 37.0 seconds. File lengths (MBytes): RWF= 943 Int= 0 D2E= 0 Chk= 3 Scr= 1 i do not know how to deal with the quesiton.what does "D2PCM-2 allocation failure" means? why the "Sum of APT charges= 0.35270 " does not equal to zero? eager to wait for your reply!thank you very much! have a nice time everyday! your sincere :guoyong 2004 6 25 --------------------------------- Do You Yahoo!? 100UWSJOd9;2;9;SC#?QE;"5gSJWTVz@)H]#! From chemistry-request@ccl.net Mon Jun 28 11:18:55 2004 Received: from smtp2.es.uci.edu (smtp2.es.uci.edu [128.200.80.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5SGIshH030728 for ; Mon, 28 Jun 2004 11:18:54 -0500 Received: from frenkel.ps.uci.edu (frenkel.ps.uci.edu [128.200.11.119]) by smtp2.es.uci.edu (8.12.8/8.12.8) with ESMTP id i5SGNo1o003837 for ; Mon, 28 Jun 2004 09:23:54 -0700 Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz:at:mail.rochester.edu Organization: university of california at Irvine To: chemistry:at:ccl.net Subject: problem of compiling charmm on 64 bit Opteron Date: Mon, 28 Jun 2004 09:22:00 -0400 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200406280922.00723.wzhuang:at:uci.edu> X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=1.7 required=7.5 tests=DATE_IN_PAST_03_06, IMPRONONCABLE_2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i5SGIthH030734 Hi, when I compile charmm c30b2 on a 64 bit Opteron beowulf cluster running SUSE 9.0. I used g77 compiler. at first it gave the error message like ************************ f771: error: -malign-double makes no sense in the 64bit mode *************************** so I took off the flag "-malign-doubl" in build/gnu/Makefile_gnu. and then the compilation went through. but then when I run a minimization. it broke down and gave the error message as: ***** == PRIMARY == SPACE FOR 7581700 ATOM PAIRS AND 0 GROUP PAIRS VEHEAP> Expanding heap size by12042240 words. Segmentation fault ******************* the strange thing is, I compile charmm on a AMD athelon cluster running SUSE 9.0 ( with and without that two flags ), and it works fine. would anyone tell me what is going on here? wei zhuang From chemistry-request@ccl.net Mon Jun 28 21:07:34 2004 Received: from smtp3.es.uci.edu (smtp3.es.uci.edu [128.200.80.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i5T27XhH027805 for >ccl.net>; Mon, 28 Jun 2004 21:07:33 -0500 Received: from 128.200.204.158 (dhcp-204158.bio.uci.edu [128.200.204.158]) by smtp3.es.uci.edu (8.12.8/8.12.8) with ESMTP id i5T2CbOF019774 for >ccl.net>; Mon, 28 Jun 2004 19:12:39 -0700 Date: Mon, 28 Jun 2004 19:12:34 -0700 From: Qiang Lu >uci.edu> X-Mailer: The Bat! (v1.62r) Reply-To: Qiang Lu >uci.edu> Organization: UCI MBB X-Priority: 3 (Normal) Message-ID: <1684412785.20040628191234<>uci.edu> To: chemistry<>ccl.net Subject: Re[2]: CCL:how to calculate proton dissociation energy in GAUSSIAN03 In-Reply-To: <40E0297A.9000903<>trentu.cA> References: <6039937.20040617140858<>uci.edu> <40D36714.7090100<>trentu.cA> <996418025.20040618185904<>uci.edu> <40E0297A.9000903<>trentu.cA> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-NACS_ES-MailScanner: No viruses found X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi Errol and Shobe, Thank you for the correction. I successively get the proton dissociation energy. I good explanation about this can be also found in J. Phys. Chem. 1996, 100, 15105-15110. This could help to other people who might be interested in this topic. I have a further question about the proton dissociation energy. What if I have three CYS bind to ZN(2+), could I calculation the proton dissociation energy of these three CYS in the same time. One structure is all the CYS contain thiol and another structure is that all the CYS contain thiolate. The thermal energy of H+, (3/2)kT, will be considered finally. -- Best regards, Qiang mailto:qiangl<>uci.edu =================Original message text=============== 2004 June 28 Hello, You could simply do a single point on H+ (or any single-atom species, like a C atom, or C+, etc), but the energy of H+ is zero, since it has no electronic energy (no electronic kinetic E, no electron-electron repulsion, no electron-nucleus attraction). EL ==== Qiang Lu wrote: >Hi Errol, > >Thank you for you reply. That is what I mean. And for the energy of >H+, can I simply do a single point calculation of H+? > > > ==============End of original message text=========== From chemistry-request@ccl.net Mon Jun 28 21:51:56 2004 Received: from mailshell.com (web02.mailshell.com [209.157.66.232]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i5T2puhH031113 for >ccl.net>; Mon, 28 Jun 2004 21:51:56 -0500 Received: (qmail 14553 invoked by uid 99); 29 Jun 2004 02:57:05 -0000 Message-ID: <1088477825.40e0da814e215<>www.mailshell.com> Date: Mon, 28 Jun 2004 19:57:05 -0700 X-Priority: 3 (Normal) From: >fekete.mailshell.com> To: CHEMISTRY<>ccl.net Subject: MOPAC charges in excited state In-Reply-To: <20040615131236.84787.qmail<>web60905.mail.yahoo.com> MIME-Version: 1.0 Content-Type: text/plain Content-Transfer-Encoding: 8bit User-Agent: Mailshell.com X-Spam-Status: No, hits=2.0 required=7.5 tests=NO_REAL_NAME,PRIORITY_NO_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I'm trying to get atomic charges for excited states with MOPAC v6 - but the charges output always seem to be that of the ground state (and the ones when MULLIKEN keyword is given look total garbage, not even summing up to any integer value)! Is there any way to get them correctly with this program? -- Zoli Fekete _______________________________________________________ The FREE service that prevents junk email http://www.mailshell.com