From chemistry-request@ccl.net Fri Nov 19 11:44:35 2004 Received: from web15404.mail.cnb.yahoo.com (web15404.mail.cnb.yahoo.com [202.43.216.207]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAJGiXnj021148 for ; Fri, 19 Nov 2004 11:44:34 -0500 Message-ID: <20041119165835.4791.qmail)at(web15404.mail.cnb.yahoo.com> Received: from [61.179.12.213] by web15404.mail.cnb.yahoo.com via HTTP; Sat, 20 Nov 2004 00:58:35 CST Date: Sat, 20 Nov 2004 00:58:35 +0800 (CST) From: Jinsong Zhao Subject: CCL: block unscaled weigths (BUW) To: CCL MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=3.8 required=7.5 tests=DATE_IN_PAST_12_24, MK_YAHOO_REDIR_01,RCVD_IN_SBL,WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, Block unscaled weigths (BUW) is a chemometrics way used to pretreat data blocks obtained from GRID or other grid/CoMFA like ways. It's useful in establishing a good QSAR model. It has been implemented in GOLPE, and firstly introduced in J. Med. Chem. 2000, 43, 3033-3044. I am very interested in BUW, for I am doing something with the data block obtained from GRID. However, I can not afford GOLPE, I have to implement this method in my own way. But, I can not find a algorithm to implement BUW, even can not find a detail description. Does anyone here have experience with such method? Any suggestion and/or comments will be really appreciated. Thank you very much for your kindly consideration on this matter. Best wishes, Jinsong _________________________________________________________ Do You Yahoo!? 150MrGzMP37h?qKQ#,4xDz43HkRt@V5nLC http://cn.rd.yahoo.com/mail_cn/tag/yisou/music/*http://music.yisou.com/ C)at(E.CwPGS&SP>!SP#,KQ1iC@MMJG1000UW#,QE;"5gSJWTVz@)H]#! http://cn.rd.yahoo.com/mail_cn/tag/1g/*http://cn.mail.yahoo.com/event/mail_1g/ From chemistry-request@ccl.net Sat Nov 20 21:33:30 2004 Received: from biscayne-one-station.mit.edu (BISCAYNE-ONE-STATION.MIT.EDU [18.7.7.80]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAL2XTos005313 for ; Sat, 20 Nov 2004 21:33:29 -0500 Received: from outgoing.mit.edu (OUTGOING-AUTH.MIT.EDU [18.7.22.103]) by biscayne-one-station.mit.edu (8.12.4/8.9.2) with ESMTP id iAL2lde1019897 for ; Sat, 20 Nov 2004 21:47:39 -0500 (EST) Received: from bpan.mit.edu (LANDAU-FOUR-O-FOUR.MIT.EDU [18.63.6.149]) (authenticated bits=0) (User authenticated as binpan!at!ATHENA.MIT.EDU) by outgoing.mit.edu (8.12.4/8.12.4) with ESMTP id iAL2lb1U018839 (version=TLSv1/SSLv3 cipher=RC4-SHA bits=128 verify=NOT) for ; Sat, 20 Nov 2004 21:47:38 -0500 (EST) Message-Id: <5.2.1.1.2.20041120214457.02094040!at!po10.mit.edu> X-Sender: binpan!at!po10.mit.edu X-Mailer: QUALCOMM Windows Eudora Version 5.2.1 Date: Sat, 20 Nov 2004 21:47:34 -0500 To: chemistry!at!ccl.net From: Bin Pan Subject: A question Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Scanned-By: MIMEDefang 2.42 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 Dear CCLers, I just read the problem mentioned at the following link: http://www.ccl.net/cgi-bin/ccl/message.cgi?1999+12+17+001 Does anyone know how to solve this problem? It seems that opt(Maxcycle=500) does not work at all although the user can specify it. Thanks! Bin. From chemistry-request@ccl.net Fri Nov 19 14:28:06 2004 Received: from cgatepro-3.mail.virginia.edu (guppy.mail.Virginia.EDU [128.143.2.218]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAJJS5nj000602 for ; Fri, 19 Nov 2004 14:28:05 -0500 Received: from [128.143.22.7] (account jtl3z!at!cgatepro-3.mail.virginia.edu) by cgatepro-3.mail.virginia.edu (CommuniGate Pro WebUser 4.1.8) with HTTP id 109203666 for chemistry!at!ccl.net; Fri, 19 Nov 2004 14:42:10 -0500 From: "Jonathan T. Lyon" Subject: ONIOM Problems with "gen" keyword To: chemistry!at!ccl.net X-Mailer: CommuniGate Pro WebUser Interface v.4.1.8 Date: Fri, 19 Nov 2004 14:42:10 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="windows-1252" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=1.0 required=7.5 tests=IMPRONONCABLE_1 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 All, I'm having troubles running an ONIOM calculation on a M-C60 compound. This is part of my input: %chk=oniom-BS # oniom(B3LYP/gen:AM1) pseudo=read scf=qc opt freq oniom-BS 0 2 X1 X2 X1 1. X3 X1 1. X2 90. X4 X1 1. X2 90. X3 180. 0 X5 X1 1. X3 C1 X2 0. 0 X6 X1 1. X3 C1 X5 C2 0 X7 X1 1. X3 C1 X5 C3 0 X8 X1 1. X3 C1 X5 -C2 0 X9 X1 1. X3 C1 X5 -C3 0 X10 X1 1. X4 C1 X2 180. 0 X11 X1 1. X4 C1 X10 C2 0 X12 X1 1. X4 C1 X10 C3 0 X13 X1 1. X4 C1 X10 -C2 0 X13 X1 1. X4 C1 X10 -C2 0 X14 X1 1. X4 C1 X10 -C3 0 C15 X1 R X3 A X5 0. 0 H C16 X1 R X3 A X6 0. 0 H C17 X1 R X3 A X7 0. 0 L C18 X1 R X3 A X8 0. 0 H C19 X1 R X3 A X9 0. 0 L C20 X1 R X5 A X3 0. 0 H C21 X1 R X5 A X3 C2 0 H C22 X1 R X5 A X3 C3 0 L C23 X1 R X5 A X3 -C2 0 H C24 X1 R X5 A X3 -C3 0 L C25 X1 R X6 A X3 0. 0 L C26 X1 R X6 A X3 C2 0 L ................................ C71 X1 R X14 A X4 C2 0 L C72 X1 R X14 A X4 C3 0 L C73 X1 R X14 A X4 -C2 0 L C74 X1 R X14 A X4 -C3 0 L X75 X1 1. X3 B X2 0. 0 Cu75 X1 5.2 X75 0. X3 B 1 H R 3.52429 A 20.5346 B 31.71747441 C1 63.434948823 C2 72.0 C3 144.0 Cu 0 sdd C 0 6-311++G** **** Cu 0 sdd **** Whe I run the calculations, I get the following error: Warning! Cu atom 61 has 11 valence electrons but only 4 basis functions. This is less than a minimal basis set! IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 ScaDFX= 1.000000 1.000000 1.000000 1.000000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 NAtoms= 61 NActive= 61 NUniq= 18 SFac= 5.66D+00 NAtFMM= 60 Big=F Leave Link 301 at Fri Nov 19 09:59:21 2004, MaxMem= 6291456 cpu: 0.4 (Enter /uva/lib/gaussian/g03/l401.exe) Simple Huckel Guess. NBasis= 244 NMin= 249 so simple Huckel guess is impossible. Error termination via Lnk1e in /uva/lib/gaussian/g03/l401.exe at Fri Nov 19 09 59:23 2004. Job cpu time: 0 days 0 hours 0 minutes 9.3 seconds. File lengths (MBytes): RWF= 31 Int= 0 D2E= 0 Chk= 1 Scr= 1 I've discovered that the pseudopotential being read needs to be given before the basis sets (otherwise I get an error that 6-311++G** is an unknown pseudopotential), but the program still is having troubles reading the correct basis set. Is there something special I need to do to use both the ONIOM program and the "gen" keyword? Thanks, Jon Lyon jtl3z!at!virginia.edu From chemistry-request@ccl.net Fri Nov 19 19:35:18 2004 Received: from smtp4.es.uci.edu (smtp4.es.uci.edu [128.200.80.7]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAK0ZHnj021324 for >ccl.net>; Fri, 19 Nov 2004 19:35:18 -0500 Received: from [127.0.0.1] (host124.ps.uci.edu [128.200.11.124]) by smtp4.es.uci.edu (8.12.8/8.12.8) with ESMTP id iAK0n4wi019152 for >ccl.net>; Fri, 19 Nov 2004 16:49:06 -0800 Date: Fri, 19 Nov 2004 16:49:01 -0800 From: Tomoyuki Hayashi >uci.edu> To: CHEMISTRY<>ccl.net Subject: CCL: good parameters for chloroform, acetonitrile, and DMSO used with the CHARMM force field for NMA Message-Id: <20041119162747.62E6.TOMOYUKH<>uci.edu> MIME-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: Becky! ver. 2.11.02 [ja] X-NACS_ES-MailScanner: No viruses found Dear All: I want to do a simulation of N-methyl acetamide(NMA) in several solvents, but I can't find the parameters for chloroform, acetonitrile and DMSO in CHARMM. Can anyone give me the best force field parameters for them combined with the CHARMM force field (found in top_all22_model.inp file) for NMA? -- Tomoyuki Hayashi >uci.edu> From chemistry-request@ccl.net Mon Nov 22 03:30:14 2004 Received: from charybdis.rus.uni-stuttgart.de (charybdis.rus.uni-stuttgart.de [129.69.1.58]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAM8UCJm024604 for ; Mon, 22 Nov 2004 03:30:13 -0500 Received: from localhost (localhost [127.0.0.1]) by charybdis.rus.uni-stuttgart.de (Postfix) with ESMTP id B9F191878F8 for ; Mon, 22 Nov 2004 09:44:23 +0100 (CET) Received: from charybdis.rus.uni-stuttgart.de ([127.0.0.1]) by localhost (charybdis [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 18500-01-83 for ; Mon, 22 Nov 2004 09:44:12 +0100 (CET) Received: from uni-stuttgart.de (mbox.rus.uni-stuttgart.de [129.69.1.9]) by charybdis.rus.uni-stuttgart.de (Postfix) with ESMTP id 75A2318B552 for ; Mon, 22 Nov 2004 09:44:06 +0100 (CET) X-Virus-Scanned: by mbox.uni-stuttgart.de Received: from [129.69.145.98] (account itbptr*at*itb.uni-stuttgart.de HELO ITBNTW31.itb.uni-stuttgart.de) by uni-stuttgart.de (CommuniGate Pro SMTP 4.2.5) with ESMTP id 13009926 for chemistry*at*ccl.net; Mon, 22 Nov 2004 09:43:31 +0100 Message-Id: <6.0.0.22.1.20041122093608.023ecdc8*at*mbox.uni-stuttgart.de> X-Sender: itbptr*at*itb.uni-stuttgart.de@mbox.uni-stuttgart.de X-Mailer: QUALCOMM Windows Eudora Version 6.0.0.22 Date: Mon, 22 Nov 2004 09:38:45 +0100 To: chemistry*at*ccl.net From: Peter Trodler Subject: calculation of pKa values Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-Virus-Scanned: by amavisd-new at charybdis.rus.uni-stuttgart.de X-Spam-Status: No, hits=3.9 required=7.5 tests=MY_BAD_DOT,NO_RDNS2 autolearn=no version=2.61 X-Spam-Level: X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear ccl users, there are several tools to calculate pKa values of residues of a protein (TITRA,MCCE,MEAD,PDB2PQR,WHATIF). I am thinking which of this tools i should use to protonate the residues by pKa value, because the results are different, especially in the active site of proteins, and I dont want to protonate by standard pKa values. It is not easy to compare the results with experimental data, especially the protonation of ASP and GLU. Has somebody already compared this tools and can recommend me which tool I should use ? I appreciate any help. Best regards, Peter Trodler From chemistry-request@ccl.net Fri Nov 19 12:05:50 2004 Received: from mailservice.tudelft.nl (mailservice.tudelft.nl [130.161.131.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAJH5enj022978 for ; Fri, 19 Nov 2004 12:05:40 -0500 Received: from localhost (localhost [127.0.0.1]) by rav.antivirus (Postfix) with ESMTP id 7EA9B8003C for ; Fri, 19 Nov 2004 18:19:44 +0100 (CET) Received: from mail.dct.tudelft.nl (tnw-dct1.dct.tudelft.nl [130.161.196.201]) by mx4.tudelft.nl (Postfix) with ESMTP id 4EE3A80030 for ; Fri, 19 Nov 2004 18:19:43 +0100 (CET) Received: from TNW-DCT1/SpoolDir by mail.dct.tudelft.nl (Mercury 1.48); 19 Nov 04 18:19:43 +0200 Received: from SpoolDir by TNW-DCT1 (Mercury 1.48); 19 Nov 04 18:18:09 +0200 From: "Martijn Zwijnenburg" Organization: Delft University of Technology (TNW-DCT) To: chemistry[at]ccl.net Date: Fri, 19 Nov 2004 18:18:08 +0100 MIME-Version: 1.0 Subject: CCl: CIS opt on G03 problem Message-ID: <419E38DD.14386.FB0D524[at]mail.dct.tudelft.nl> Priority: normal X-mailer: Pegasus Mail for Windows (4.21b) Content-type: Multipart/Alternative; boundary="Alt-Boundary-14395.263247328" X-Virus-Scanned: by amavisd-new at tudelft.nl X-Spam-Status: No, hits=3.4 required=7.5 tests=BAD_X_HEADERS,HTML_50_60, HTML_MESSAGE,HTML_TITLE_EMPTY,IMPRONONCABLE_1,MK_BAD_HTML_13 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --Alt-Boundary-14395.263247328 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body Dear all, I'm trying to do an CIS optimization on a closed shell molecule using G03 B.05 and the calc stops with the following error while calculating the second derivatives: Doing CIS second derivatives. This link is doing 39 degrees of freedom Form MO integral derivatives with frozen-active canonical formalism. CisSec: MDV= 6291358 Frozen orbitals handled with amplitudes over full window. Frozen-core window: NFC= 28 NFV= 0. The selected state is a singlet Computing gradients using direct method. Cannot handle 2e integral symmetry, ISym2E=1. CISAX: IP= 1 NPass= 1 NMax= 39. CISAX will form 39 AO SS matrices at one time. NMat= 39 NSing= 39. Symmetry not used in FoFDir. MinBra= 0 MaxBra= 2 Meth= 1. IRaf= 0 NMat= 39 IRICut= 39 DoRegI=T DoRafI=T ISym2E= 0 JSym2E=0. Symmetry is being used. 36 vectors were produced by pass 0. AX will form 36 AO Fock derivatives at one time. 36 vectors were produced by pass 1. 36 vectors were produced by pass 2. 36 vectors were produced by pass 3. 36 vectors were produced by pass 4. 36 vectors were produced by pass 5. 36 vectors were produced by pass 6. 35 vectors were produced by pass 7. 18 vectors were produced by pass 8. 4 vectors were produced by pass 9. 1 vectors were produced by pass 10. Inv2: IOpt= 1 Iter= 1 AM= 6.49D-14 Conv= 1.00D-12. Inverted reduced A of dimension 310 with in-core refinement. Max Tx.T = 0.001666563882 for Degree = 1 Tx not orthogonal to T. Error termination via Lnk1e in /usr/local/opt/g03/l1014.exe at Fri Nov 19 18:03:34 2004. Job cpu time: 0 days 3 hours 14 minutes 13.5 seconds. File lengths (MBytes): RWF= 201 Int= 0 D2E= 0 Chk= 3 Scr= 1 Does anybody know why this error occurs and how it can be resolved? Many thanks in advance, Martijn Zwijnenburg -- Martijn Zwijnenburg PhD Ceramic Membrane Centre "The Pore" DelftChemTech, Delft University of Technology Julianalaan 136, 2628 BL Delft The Netherlands m.a.zwijnenburg[at]tnw.tudelft.nl Phone : + 31 1527 89418 (office) + 31 7039 63701 (home) Fax : + 31 1527 84289 http://www.dct.tudelft.nl/thepore/people/M.A.Zwijnenburg.html --Alt-Boundary-14395.263247328 Content-type: text/html; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body
Dear all,

I'm trying to do an CIS optimization on a closed shell molecule using G03 B.05 and the calc stops with the following error while calculating the second derivatives:

Doing CIS second derivatives.
This link is doing    39 degrees of freedom
Form MO integral derivatives with frozen-active canonical formalism.
CisSec: MDV=       6291358
Frozen orbitals handled with amplitudes over full window.
Frozen-core window:  NFC=  28 NFV=   0.
The selected state is a singlet
Computing gradients using direct method.
Cannot handle 2e integral symmetry, ISym2E=1.
CISAX:  IP=  1 NPass=   1 NMax=  39.
CISAX will form  39 AO SS matrices at one time.
NMat= 39 NSing= 39.
Symmetry not used in FoFDir.
MinBra= 0 MaxBra= 2 Meth= 1.
IRaf=       0 NMat=  39 IRICut=      39 DoRegI=T DoRafI=T ISym2E= 0 JSym2E=0.
Symmetry is being used.
   36 vectors were produced by pass  0.
AX will form  36 AO Fock derivatives at one time.
   36 vectors were produced by pass  1.
   36 vectors were produced by pass  2.
   36 vectors were produced by pass  3.
   36 vectors were produced by pass  4.
   36 vectors were produced by pass  5.
   36 vectors were produced by pass  6.
   35 vectors were produced by pass  7.
   18 vectors were produced by pass  8.
    4 vectors were produced by pass  9.
    1 vectors were produced by pass 10.
Inv2:  IOpt= 1 Iter= 1 AM= 6.49D-14 Conv= 1.00D-12.
Inverted reduced A of dimension  310 with in-core refinement.
Max Tx.T =      0.001666563882 for Degree =      1
Tx not orthogonal to T.
Error termination via Lnk1e in /usr/local/opt/g03/l1014.exe at Fri Nov 19 18:03:34 2004.
Job cpu time:  0 days  3 hours 14 minutes 13.5 seconds.
File lengths (MBytes):  RWF=    201 Int=      0 D2E=      0 Chk=      3 Scr=      1

Does anybody know why this error occurs and how it can be resolved?

Many thanks in advance,

Martijn Zwijnenburg

--
Martijn Zwijnenburg PhD
Ceramic Membrane Centre "The Pore"
DelftChemTech, Delft University of Technology
Julianalaan 136, 2628 BL Delft
The Netherlands
m.a.zwijnenburg[at]tnw.tudelft.nl
Phone  : + 31 1527 89418 (office)
              + 31 7039 63701 (home)
Fax      : + 31 1527 84289
http://www.dct.tudelft.nl/thepore/people/M.A.Zwijnenburg.html
--Alt-Boundary-14395.263247328-- From chemistry-request@ccl.net Sat Nov 20 01:59:24 2004 Received: from smtp111.mail.sc5.yahoo.com (smtp111.mail.sc5.yahoo.com [66.163.170.9]) by server.ccl.net (8.12.8/8.12.8) with SMTP id iAK6xN2G011039 for ; Sat, 20 Nov 2004 01:59:23 -0500 Received: from unknown (HELO ?192.168.11.112?) (gaire?catala@213.98.129.17 with login) by smtp111.mail.sc5.yahoo.com with SMTP; 20 Nov 2004 07:13:28 -0000 Date: Sat, 20 Nov 2004 08:13:26 +0100 From: Miquel Duran To: chemistry{at}ccl.net Subject: [iqc udg] Gaussian: Xeon Nocona vs. Opteron Message-Id: <20041120080935.24FC.QUEL{at}iqc.udg.es> MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1" X-Mailer: Becky! ver. 2.11.02 [en] 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 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id iAK6xO2G011045 Dear CCLers, we are about to purchase a new cluster, and have got offers involving dual-cpu Opterons and Noconas. We would like very much to see some timings on the performance of Gaussian 03 on these CPUs. Even thouh raw performance (i.e., specfp's) are available, actual results for Gaussian might be different. Any information will be very helpful. Thanks in advance. Miquel Duran Departament de Qummica i Institut de Qummica Computacional Universitat de Girona, Spain From chemistry-request@ccl.net Fri Nov 19 11:30:56 2004 Received: from mxsf13.cluster1.charter.net (mxsf13.cluster1.charter.net [209.225.28.213]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAJGUrnj020182 for ; Fri, 19 Nov 2004 11:30:53 -0500 Received: from mxip06.cluster1.charter.net (mxip06a.cluster1.charter.net [209.225.28.136]) by mxsf13.cluster1.charter.net (8.12.11/8.12.11) with ESMTP id iAJGiu6U020347 for ; Fri, 19 Nov 2004 11:44:57 -0500 Received: from 24.247.172.122.bay.mi.chartermi.net (HELO inspiron9100) (24.247.172.122) by mxip06.cluster1.charter.net with ESMTP; 19 Nov 2004 11:44:56 -0500 Message-Id: <3khj1f$crvogm..at..mxip06a.cluster1.charter.net> X-Ironport-AV: i="3.87,100,1099285200"; d="scan'208"; a="432005654:sNHT11830604" From: "Jim Kress" To: Subject: Solvate in ArgusLab Date: Fri, 19 Nov 2004 11:44:55 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.5510 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Thread-Index: AcTM1T3K2UlS0sacR2+aq2Fc2Tu0OABgUsRQ In-Reply-To: <20041117123825.GK1457..at..leitl.org> X-Spam-Status: No, hits=2.6 required=7.5 tests=RCVD_IN_DYNABLOCK, RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net In the latest version of ArgusLab there is a 'solvate' command under the Tools menu. Anyone know how to use it? When I load a molecule and then issue the solvate command, I get an error message and then the program hangs. Jim From chemistry-request@ccl.net Mon Nov 22 10:58:13 2004 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAMFwCXu005217 for ; Mon, 22 Nov 2004 10:58:12 -0500 Received: from localhost (localhost.localdomain [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 13B3625AE84; Mon, 22 Nov 2004 11:12:29 -0500 (EST) Received: from smtpgw.sud-chemieinc.com ([127.0.0.1]) by localhost (smtpgw.sud-chemieinc.com [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 24114-02; Mon, 22 Nov 2004 11:12:28 -0500 (EST) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 8FEDB25AE80; Mon, 22 Nov 2004 11:12:28 -0500 (EST) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.6713); Mon, 22 Nov 2004 11:10:18 -0500 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" X-MimeOLE: Produced By Microsoft Exchange V6.0.6556.0 Subject: RE: ONIOM Problems with "gen" keyword Date: Mon, 22 Nov 2004 11:10:17 -0500 Message-ID: <9DD56492790889439F731F5BD6DACA000492E6DF..at..srvkyem1.americas.sc-world.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: ONIOM Problems with "gen" keyword Thread-Index: AcTQjhVgg6VVplW5T1Cu6nHvdMcATwAHzjQw From: "Shobe, David" To: "Jonathan T. Lyon" , X-OriginalArrivalTime: 22 Nov 2004 16:10:18.0944 (UTC) FILETIME=[C2CE5C00:01C4D0AD] X-Spam-Status: No, hits=4.0 required=7.5 tests=IMPRONONCABLE_1,NO_RDNS2 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 iAMFwDXu005224 It looks like you have the basis set information after the pseudopotential information. The basis set information should come *before* the pseudopotential information. --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request..at..ccl.net]On Behalf Of Jonathan T. Lyon Sent: Friday, November 19, 2004 2:42 PM To: chemistry..at..ccl.net Subject: CCL:ONIOM Problems with "gen" keyword Hi All, I'm having troubles running an ONIOM calculation on a M-C60 compound. This is part of my input: %chk=oniom-BS # oniom(B3LYP/gen:AM1) pseudo=read scf=qc opt freq oniom-BS 0 2 X1 X2 X1 1. X3 X1 1. X2 90. X4 X1 1. X2 90. X3 180. 0 X5 X1 1. X3 C1 X2 0. 0 X6 X1 1. X3 C1 X5 C2 0 X7 X1 1. X3 C1 X5 C3 0 X8 X1 1. X3 C1 X5 -C2 0 X9 X1 1. X3 C1 X5 -C3 0 X10 X1 1. X4 C1 X2 180. 0 X11 X1 1. X4 C1 X10 C2 0 X12 X1 1. X4 C1 X10 C3 0 X13 X1 1. X4 C1 X10 -C2 0 X13 X1 1. X4 C1 X10 -C2 0 X14 X1 1. X4 C1 X10 -C3 0 C15 X1 R X3 A X5 0. 0 H C16 X1 R X3 A X6 0. 0 H C17 X1 R X3 A X7 0. 0 L C18 X1 R X3 A X8 0. 0 H C19 X1 R X3 A X9 0. 0 L C20 X1 R X5 A X3 0. 0 H C21 X1 R X5 A X3 C2 0 H C22 X1 R X5 A X3 C3 0 L C23 X1 R X5 A X3 -C2 0 H C24 X1 R X5 A X3 -C3 0 L C25 X1 R X6 A X3 0. 0 L C26 X1 R X6 A X3 C2 0 L >................................ C71 X1 R X14 A X4 C2 0 L C72 X1 R X14 A X4 C3 0 L C73 X1 R X14 A X4 -C2 0 L C74 X1 R X14 A X4 -C3 0 L X75 X1 1. X3 B X2 0. 0 Cu75 X1 5.2 X75 0. X3 B 1 H R 3.52429 A 20.5346 B 31.71747441 C1 63.434948823 C2 72.0 C3 144.0 Cu 0 sdd C 0 6-311++G** **** Cu 0 sdd **** Whe I run the calculations, I get the following error: Warning! Cu atom 61 has 11 valence electrons but only 4 basis functions. This is less than a minimal basis set! IExCor= 0 DFT=F Ex=HF Corr=None ExCW=0 ScaHFX= 1.000000 ScaDFX= 1.000000 1.000000 1.000000 1.000000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 NAtoms= 61 NActive= 61 NUniq= 18 SFac= 5.66D+00 NAtFMM= 60 Big=F Leave Link 301 at Fri Nov 19 09:59:21 2004, MaxMem= 6291456 cpu: 0.4 (Enter /uva/lib/gaussian/g03/l401.exe) Simple Huckel Guess. NBasis= 244 NMin= 249 so simple Huckel guess is impossible. Error termination via Lnk1e in /uva/lib/gaussian/g03/l401.exe at Fri Nov 19 09 59:23 2004. Job cpu time: 0 days 0 hours 0 minutes 9.3 seconds. File lengths (MBytes): RWF= 31 Int= 0 D2E= 0 Chk= 1 Scr= 1 I've discovered that the pseudopotential being read needs to be given before the basis sets (otherwise I get an error that 6-311++G** is an unknown pseudopotential), but the program still is having troubles reading the correct basis set. Is there something special I need to do to use both the ONIOM program and the "gen" keyword? Thanks, Jon Lyon jtl3z..at..virginia.edu -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY..at..ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST..at..ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow..at..nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Mon Nov 22 10:26:26 2004 Received: from mailhub.cs.uoguelph.ca (mailhub.cs.uoguelph.ca [131.104.96.75]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id iAMFQPXu002214 for >ccl.net>; Mon, 22 Nov 2004 10:26:26 -0500 Received: from max0q2aifg2apps ([131.104.156.125]) by mailhub.cs.uoguelph.ca (8.13.1/8.13.1) with ESMTP id iAMFeUqA009010 for ; Mon, 22 Nov 2004 10:40:39 -0500 Message-Id: <200411221540.iAMFeUqA009010=at=mailhub.cs.uoguelph.ca> From: "Peng Liu" To: Subject: CASSCF Calculation Date: Mon, 22 Nov 2004 10:40:30 -0500 Organization: University of Guelph MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Mailer: Microsoft Office Outlook, Build 11.0.6353 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2180 Thread-Index: AcTQqZiiWu9dvAkhSP2iZ9j4pHa8Mg== X-Scanned-By: MIMEDefang 2.44 X-Spam-Status: No, hits=3.0 required=7.5 tests=NO_RDNS2 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, all: I am trying to do the UHF-NO-CASSCF calculation using Gaussian 98 on an excited aromatic structure. But I've got very different results of the energy in different computers using the same input file. I tried the same version of G98 (Rev. A.11) on two alpha computers and didn't get the same result either. I think the only difference may be the compiler and the version of ATLAS library during the installation, but how can that make so much difference? I've compared the output files. The differences first occur during the output of the natural orbitals in the UHF calculation. I really appreciate any help. Best regards, Peng Liu