From chemistry-request@ccl.net Fri May 13 10:40:19 2005 Received: from proxy1.uh.cu (smtp1.uh.cu [200.55.139.212]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4DEeBkG003417 for ; Fri, 13 May 2005 10:40:14 -0400 Received: from localhost (localhost.localdomain [127.0.0.1]) by proxy1.uh.cu (Postfix) with ESMTP id AF4B42FDC8 for ; Fri, 13 May 2005 10:43:51 -0400 (CDT) Received: from fq.uh.cu (unknown [192.168.3.4]) by proxy1.uh.cu (Postfix) with ESMTP id 6FDC52FDC4 for ; Fri, 13 May 2005 10:43:51 -0400 (CDT) Received: from fq.uh.cu (IDENT:25@localhost [127.0.0.1]) by fq.uh.cu (8.12.4/8.12.4/JP) with ESMTP id j4DAaJJZ009221 for ; Fri, 13 May 2005 06:36:19 -0400 Received: from localhost (david@localhost) by fq.uh.cu (8.12.4/8.12.4/Submit) with ESMTP id j4DAERYa008478; Fri, 13 May 2005 06:14:27 -0400 Date: Fri, 13 May 2005 06:14:23 -0400 (CDT) From: David Santos Carballal To: lhhu {} yangtze.hku.hk Cc: chemistry {} ccl.net Subject: Re: CCL:Tinker input file 2 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by AMaViS snapshot-20020300 X-Spam-Status: No, score=0.1 required=5.0 tests=FORGED_RCVD_HELO autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear Holly: I really don't know any other way to assign it automatically. I always do it manually. I had tried with babel, but it's atoms types are diferent to those of TINKER. My suggest is open the cartesian coordinate file and the force field file (with extension .prm in the folder params of TINKER folder) and put the numbers. Good luck: David Santos Carballal On Thu, 12 May 2005 lhhu {} yangtze.hku.hk wrote: > > Dear David, > > Thank you very much for your reply. Actually I tried the way you told me > before. I think the most trouble thing is that I have to assign those > atomic force field types manually. Is there any automatic way to do > this? I am wondering if the molecules are really big, how it can be done > in this way? It is really time consuming. > > Best wishes, > > Holly > > On Wed, 11 May 2005, David Santos Carballal wrote: > > > I forgot: > > You would find the pdbxyz.exe in the bin directory of TINKER, if you run > > it from Windows > > > > David Santos Carballal > > > > On Wed, 11 May 2005 lhhu {} yangtze.hku.hk wrote: > > > >> > >> Dear all CCLers, > >> > >> I would like to use free TINKER to calculated molecular dynamics. But the > >> input file of tinker seems difficult to generate because the int or xyz > >> file need to be assigned force field atom type first. Can anyone tell me > >> about the most convenient way to generate the input xyz or int file? Is > >> there any free program I can use? > >> > >> Thank you very much, > >> > >> Holly > >> > >> > >> > >> Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST {} ccl.net > >> HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >> > >> use the Web based form from CCL Home Page > >> > >> > >> > >> > >> > > > > > > -= 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 {} ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST {} ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Fri May 13 06:48:35 2005 Received: from ams1.ulsop.ac.uk (ams1.ulsop.ac.uk [194.66.95.40]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4DAmVsk023193 for ; Fri, 13 May 2005 06:48:31 -0400 Received: from [194.66.95.148] by ams1.ulsop.ac.uk (GMS 10.03.3304/NU8488.01.32b4d6e5) with SMTP id babifaaa for chemistry {} ccl.net; Fri, 13 May 2005 10:43:44 +0100 From: "Mire Zloh" To: Subject: NMR based modelling of DNA-protein complexes Date: Fri, 13 May 2005 10:47:00 +0100 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0005_01C557A9.1777E4B0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1478 X-AntiSpam: Checked for restricted content by Gordano's AntiSpam Software X-Spam-Status: No, score=0.0 required=5.0 tests=HTML_MESSAGE autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0005_01C557A9.1777E4B0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Dear CCLers, we are studying complexes between oligonucleotides and peptide-anthraquinone conjugates using homonuclear NMR. We are hoping to build NMR based models, and we are finding difficult to decide which software to use. Could you please recommend a software for distance constraints generation and structure calculation that could cope with these combinations of molecules (DNA, peptides linked to anthraquinone). Thank you very much. Best wishes, Mire =================================================== Dr Mire Zloh BSc, Department of Pharmaceutical & Biological Chemistry The School of Pharmacy University of London 29/39 Brunswick Square London WC1N 1AX Tel: +44 (0)207 753 5879 Fax: +44 (0)207 753 5964 http://www.ulsop.ac.uk/depts/pharmchem/zloh.html ==================================================== ------=_NextPart_000_0005_01C557A9.1777E4B0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear=20 CCLers,
 
we = are studying complexes=20 between oligonucleotides and peptide-anthraquinone conjugates using = homonuclear=20 NMR. We are hoping to build NMR based models, and we are finding = difficult to=20 decide which software to use.
 
Could you please = recommend a=20 software for distance constraints generation and structure calculation = that=20 could cope with these combinations of molecules (DNA, peptides linked to = anthraquinone).
 
Thank you very=20 much.
 
Best=20 wishes,
 
Mire
 

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D

Dr Mire=20 Zloh BSc,

Department=20 of Pharmaceutical & Biological Chemistry

The School=20 of Pharmacy

University=20 of London

29/39=20 Brunswick Square

London

WC1N=20 1AX

Tel: +44=20 (0)207 753 5879

Fax: +44=20 (0)207 753 5964

http://www.ulsop.ac.uk/depts/pharmchem/zloh.html

=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D

------=_NextPart_000_0005_01C557A9.1777E4B0-- From chemistry-request@ccl.net Thu May 12 22:15:22 2005 Received: from server.ccl.net (ccl [127.0.0.1]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4D2FMLQ026013 for ; Thu, 12 May 2005 22:15:22 -0400 Received: (from apache@localhost) by server.ccl.net (8.13.1/8.13.1/Submit) id j4D2FMte026012 for chemistry {} ccl.net; Thu, 12 May 2005 22:15:22 -0400 Date: Thu, 12 May 2005 22:15:22 -0400 Message-Id: <200505130215.j4D2FMte026012 {} server.ccl.net> X-Authentication-Warning: server.ccl.net: apache set sender to chemistry-request {} ccl.net using -f From: "Bryan, , Wong" To: chemistry {} ccl.net X-Web-Message-Number: 050512221410-25936 Subject: W:molecular orbital coefficients / orthonormal gaussian basis X-Spam-Status: No, score=-2.3 required=5.0 tests=ALL_TRUSTED, FROM_ENDS_IN_NUMS autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Hi, I am using Gaussian 03 to calculate molecular orbital information for simple diatomic molecules. This is my question: at the end of the calculation, Gaussian outputs the molecular orbital coefficients. Some of these coefficients are larger than 1.0. Is this because the gaussian basis functions are normalized but not orthogonal? Phrasing the same question in a different way, do these MO coefficients correspond to the gaussian basis functions outputted by the gfprint/gfoutput keywords? Thanks, Bryan From chemistry-request@ccl.net Fri May 13 12:26:45 2005 Received: from pantheon-po08.its.yale.edu (pantheon-po08.its.yale.edu [130.132.50.50]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4DGQgHs014372 for ; Fri, 13 May 2005 12:26:42 -0400 Received: from ares.its.yale.edu (ares.its.yale.edu [130.132.52.16]) by pantheon-po08.its.yale.edu (8.12.11/8.12.11) with ESMTP id j4DFEmRX018034 (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT); Fri, 13 May 2005 11:14:48 -0400 Received: from ares.its.yale.edu (localhost [127.0.0.1]) by ares.its.yale.edu (8.12.11/8.12.11) with ESMTP id j4DFEm64013788; Fri, 13 May 2005 11:14:48 -0400 Received: from localhost (jag86@localhost) by ares.its.yale.edu (8.12.11/8.12.11/Submit) with ESMTP id j4DFEmR5013784; Fri, 13 May 2005 11:14:48 -0400 X-Authentication-Warning: ares.its.yale.edu: jag86 owned process doing -bs Date: Fri, 13 May 2005 11:14:48 -0400 (EDT) From: Jose Gascon X-X-Sender: jag86|at|ares.its.yale.edu To: "Crous Werner " cc: chemistry|at|ccl.net Subject: Re: CCL:Keeping coordinates fixed in g03 ONIOM calculation In-Reply-To: <211FDB3BAA26EA4782DC2DA769DC0A84071644|at|STBEVS04.stb.sun.ac.za> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-YaleITSMailFilter: Version 1.2b (attachment(s) not renamed) X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net Dear Werner I am not sure if this answers your question. To fix absolute coordinates you should put a " -1 " as an extra column before the coordinates you want to fix. If you want to fix internal coordinates, then using opt=modredundant should do it. Another thing, make sure your whole molecule is actually not been rotated during optimization. For that you should use the keyword nosymm. Jose Gascon Chemistry Department Yale University jose.gascon at yale.edu On Thu, 12 May 2005, Crous Werner wrote: > Hello CCL > > > > I have a problem in fixing the Cartesian coordinates in an ONIOM > calculation with g03. I have used opt=(Modredundant) and I did give the > correct input after the cartesian coordinates, but when I run the > calculation my coordinates are changed in the MM-layer and do not stay > fixed. Is it possible to fix the coordinates in g03? I would really > appreciate any help. Thank you. > > > > Werner > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Werner Crous > > MSc. student > > Department of Chemistry and Polymer Science > > University of Stellenbosch > > South Africa > > Tel. +27 218083779 > > Cell. +27 824093822 > > Email:wcrous|at|sun.ac.za > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > > From chemistry-request@ccl.net Fri May 13 12:43:17 2005 Received: from web53307.mail.yahoo.com (web53307.mail.yahoo.com [206.190.39.236]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j4DGhCei016383 for ; Fri, 13 May 2005 12:43:12 -0400 Received: (qmail 62232 invoked by uid 60001); 13 May 2005 15:43:11 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=bgkvO9/QFbuCfRzPd3kUl9iiv2s5qisDWJzScZCTxTZ2kqPg97E+M5FL7wUx/woXagaWxS9CcPCFhMhauHuYkg61VFT2fmm49ALW1g0GM+VTYU1EjUT430DL60DBu5cL2iEbUowRS+4gj+o+6vRFmONKBzCMi0yTTm3q9+VGMvg= ; Message-ID: <20050513154311.62229.qmail = = = web53307.mail.yahoo.com> Received: from [144.16.64.4] by web53307.mail.yahoo.com via HTTP; Fri, 13 May 2005 08:43:11 PDT Date: Fri, 13 May 2005 08:43:11 -0700 (PDT) From: Chaitanya Krishna A Subject: CCL:W:Transition state location for heterogeneous reaction in Gaussian To: CHEMISTRY = = = ccl.net In-Reply-To: <200505120613.j4C6DGIP026469 = = = server.ccl.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, score=2.3 required=5.0 tests=DNS_FROM_RFC_ABUSE, DNS_FROM_RFC_POST,FROM_ENDS_IN_NUMS autolearn=no version=3.0.3 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net hi Xiaobo, > I have problems locating transition states of > heterogeneous reactions. The transition state > structures are usually complicated for reactions > involving around 20 atoms including the reactant and > catalyst cluster. Does anybody have experience > locating this type of TS? What could be a good > initial gemetry guess? Is Gaussin keyword OPT=QST2 > or QST3 useful in this case? I have recently used Gaussian and QST2 and QST3 were of great help in locating the TS. Try using them. Should make your life a lot simpler. Regards, Chaitanya. __________________________________ Yahoo! Mail Mobile Take Yahoo! Mail with you! Check email on your mobile phone. http://mobile.yahoo.com/learn/mail From chemistry-request@ccl.net Fri May 13 16:24:07 2005 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4DKNw98010272 for ; Fri, 13 May 2005 16:24:03 -0400 Received: by CELEBRIS04 with Internet Mail Service (5.5.2655.55) id ; Fri, 13 May 2005 15:35:16 -0300 Message-ID: From: Ian Hovell To: "'chemistry'" Subject: CCL: specifying number of processors for Gaussian03W Date: Fri, 13 May 2005 15:35:11 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2655.55) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C557EA.7F049E20" X-Spam-Status: No, score=0.1 required=5.0 tests=HTML_50_60,HTML_MESSAGE autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C557EA.7F049E20 Content-Type: text/plain; charset="iso-8859-1" Dear CCLers, I am running Gaussian03W, which does not support parallel processing, in a windows 2000 environment using a dual processed Dell workstation. Would I see a significate increase in throughput performance if I used a Gaussian03W version which supported parallel processing? TIA Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cincia e da Tecnologia- MCT Avenida Ip, No 900 - Cidade Universitaria Ilha do Fundo Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 7344 ou 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell..at..cetem.gov.br ------_=_NextPart_001_01C557EA.7F049E20 Content-Type: text/html; charset="iso-8859-1"
Dear CCLers,
I am running Gaussian03W, which does not support parallel processing, in a windows 2000 environment using a dual processed Dell workstation. Would I see a significate increase in throughput performance if I used a Gaussian03W version which supported parallel processing?
TIA
Ian Hovell - Ph.D.
NUCLEO DE MODELAGEM MOLECULAR-NMM
Centro de Tecnologia Mineral - CETEM
Ministerio da Cincia e da Tecnologia- MCT
Avenida Ip, No 900 - Cidade Universitaria
Ilha do Fundo Rio de Janeiro RJ Brasil
CEP 21941-590
tel 00 55 (xx) 3865 7344 ou 3865 - 7216
Fax 00 55 (xx) 22602837 ou 2290-4286
e-mail hovell..at..cetem.gov.br
 
------_=_NextPart_001_01C557EA.7F049E20-- From chemistry-request@ccl.net Fri May 13 13:02:14 2005 Received: from ccc018.chemie.uni-erlangen.de (ccc018.chemie.uni-erlangen.de [131.188.128.18]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4DH2Cjc018559 for >ccl.net>; Fri, 13 May 2005 13:02:12 -0400 Received: from localhost (localhost [127.0.0.1]) by ccc018.chemie.uni-erlangen.de (Postfix) with ESMTP id 15C7534EEE for >ccl.net>; Fri, 13 May 2005 18:02:53 +0200 (CEST) Received: from ccc018.chemie.uni-erlangen.de ([127.0.0.1]) by localhost (ccc018 [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 16321-06 for >ccl.net>; Fri, 13 May 2005 18:02:44 +0200 (CEST) Received: from wwwmail.chemie.uni-erlangen.de (localhost [127.0.0.1]) by ccc018.chemie.uni-erlangen.de (Postfix) with SMTP id 2324634EE3 for >ccl.net>; Fri, 13 May 2005 18:02:44 +0200 (CEST) Received: from 131.188.174.179 (SquirrelMail authenticated user horn) by wwwmail.chemie.uni-erlangen.de with HTTP; Fri, 13 May 2005 18:02:44 +0200 (CEST) Message-ID: <33831.131.188.174.179.1116000164.squirrel<>wwwmail.chemie.uni-erlangen.de> Date: Fri, 13 May 2005 18:02:44 +0200 (CEST) Subject: Comp.Chem. and Latin From: Anselm.Horn<>chemie.uni-erlangen.de To: chemistry<>ccl.net User-Agent: SquirrelMail/1.4.1 MIME-Version: 1.0 Content-Type: text/plain;charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-Priority: 3 Importance: Normal X-Virus-Scanned: by amavisd-new at chemie.uni-erlangen.de X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net X-Spam-Status: No, score=0.2 required=5.0 tests=NO_REAL_NAME autolearn=no version=3.0.3 Dear all, first my apologies for this slightly off topic question. I wonder whether there exists a Latin dictionary or established Latin vocabulary for computer chemistry topics. Of course, the Vatican does not deal with such things, and to the best of my knowledge no comp.-chem. journal accepts articles in Latin; therefore I'm rather convinced that there does not exist any 'official' word list for quantum mechanics, force fields etc. (although most of the technical terms have Latin roots), simply because Latin is not used. However, I'd like to learn other people's opinion about that. Best regards, Anselm Horn From chemistry-request@ccl.net Fri May 13 16:03:46 2005 Received: from serenity.mcc.ac.uk (serenity.mcc.ac.uk [130.88.200.93]) by server.ccl.net (8.13.1/8.13.1) with ESMTP id j4DK3fQg008012 for ; Fri, 13 May 2005 16:03:42 -0400 Received: from tcc02.ch.man.ac.uk ([130.88.83.2] helo=TCC02) by serenity.mcc.ac.uk with smtp (Exim 4.43 (FreeBSD)) id 1DWfCq-0003yq-UR for CHEMISTRY..at..ccl.net; Fri, 13 May 2005 19:48:17 +0100 Message-ID: <000801c557eb$86430f40$02535882@TCC02> Reply-To: "Mahesh" From: "Mahesh" To: Subject: G03 ONIOM: EE Vs ME Date: Fri, 13 May 2005 19:42:32 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0005_01C557F3.E7F21A80" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2900.2527 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2527 X-UoM: Scanned by the University Mail System. See http://www.mcc.ac.uk/cos/email/scanning for details. X-Spam-Status: No, score=0.1 required=5.0 tests=HTML_50_60,HTML_MESSAGE autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0005_01C557F3.E7F21A80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear All: I am doing ONIOM caclulations as implemented in Gaussian 03 for copper = proteins (Plastocyanin), by polarising the QM by MM (electronic embedding) and without polarising = QM the MM (Mechanical embedding) starting from the same Input file. For the electronic Embedding the calculation in fine. But for the = Mechanical Embedding, the calculation terminates without any error messege.=20 The End of the output file looks like this. Fragment: 1 Trans scale: 1.0000 Rot scale: 0.0671 NRF=3D 1 NRA=3D 66 NVA=3D 393 HaveQM=3DF Convergence limit is 0.300E-04 MaxStp=3D 19428 StMxLn=3D 1.00D-04 = StpMin=3D 1.00D-06. Convergence criteria 0.00004500 0.00003000 0.00018000 = 0.00012000 Step NS ND Rises OKQ Scale Max. Force RMS Force Max. Disp. RMS = Disp. Energy Flag 233 0 0 T F 6.08D-01***********33.3755849548.68432575 = 4.10655637************* ---- 234 0 0 T F 5.00D-01***********33.3755849529.60773135 = 2.49743251************* ---- 235 0 0 T F 5.00D-01***********33.3755849514.80386568 = 1.24871625************* ---- 236 0 0 T F 6.65D-01***********33.37558495 7.40193284 = 0.62435813************* ---- 237 0 0 T F 5.00D-01***********33.37558495 4.92547679 = 0.41546736************* ---- 238 0 0 T F 6.36D-01***********33.37558495 2.46273839 = 0.2077336820605.7748208 ---- 239 0 0 T F 6.37D-01***********33.37558495 1.56563966 = 0.13206278 6266.8360699 ---- 240 0 0 T F 3.16D-01***********33.37558495 0.99655472 = 0.08406008 -24.7516875 ---- 241 0 0 T F 2.80D-01***********33.37558495 0.31506927 = 0.02657631 -30.3741662 ---- 242 0 0 T F 2.08D-01***********33.37558495 0.08809388 = 0.00743078 -33.2627979 ---- 243 0 0 T F 1.94D-01***********33.37558495 0.01835913 = 0.00154861 -48.6751008 ---- 244 0 0 F F 1.26D-01***********33.37558495 0.00356823 = 0.00030098 -61.8162325 ---- I have minimised the structure in Amber7.0 before doing the calculation. I think, the calculation is failing in the Micro Iteration.=20 But why it is not failing in the Electronic Emedding and what is the = suitable solution for this. Thanks in Advance, Regards, Mahesh S ------=_NextPart_000_0005_01C557F3.E7F21A80 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear All:
I am doing ONIOM caclulations as = implemented=20 in Gaussian 03 for copper proteins (Plastocyanin),
by polarising the QM by MM (electronic = embedding)=20 and without polarising QM the MM (Mechanical
embedding) starting from the same Input = file.
 
For the electronic Embedding the = calculation in=20 fine. But for the Mechanical Embedding,
the calculation terminates without any = error=20 messege.
 
The End of the output file looks like=20 this.
 
 Fragment:  1 Trans scale: = 1.0000 Rot=20 scale: 0.0671
 NRF=3D 1 NRA=3D  66 NVA=3D 393=20 HaveQM=3DF
 Convergence limit is  0.300E-04 MaxStp=3D 19428 = StMxLn=3D=20 1.00D-04 StpMin=3D 1.00D-06.
 Convergence=20 criteria           = 0.00004500=20 0.00003000 0.00018000 0.00012000
  Step  NS  ND Rises=20 OKQ   Scale  Max. Force  RMS Force Max. Disp.  = RMS=20 Disp.     Energy   Flag
   233   = 0  =20 0   T    F =20 6.08D-01***********33.3755849548.68432575 4.10655637*************=20 ----
   234   0   0  =20 T    F  5.00D-01***********33.3755849529.60773135=20 2.49743251************* ----
   235   = 0  =20 0   T    F =20 5.00D-01***********33.3755849514.80386568 1.24871625*************=20 ----
   236   0   0  =20 T    F  6.65D-01***********33.37558495 7.40193284=20 0.62435813************* ----
   237   = 0  =20 0   T    F  5.00D-01***********33.37558495 = 4.92547679 0.41546736************* ----
   238  =20 0   0   T    F =20 6.36D-01***********33.37558495 2.46273839 0.2077336820605.7748208=20 ----
   239   0   0  =20 T    F  6.37D-01***********33.37558495 1.56563966 = 0.13206278=20 6266.8360699 ----
   240   0   = 0  =20 T    F  3.16D-01***********33.37558495 0.99655472=20 0.08406008  -24.7516875 ----
   241   = 0  =20 0   T    F  2.80D-01***********33.37558495 = 0.31506927 0.02657631  -30.3741662 ----
   = 242  =20 0   0   T    F =20 2.08D-01***********33.37558495 0.08809388 0.00743078  -33.2627979=20 ----
   243   0   0  =20 T    F  1.94D-01***********33.37558495 0.01835913=20 0.00154861  -48.6751008 ----
   244   = 0  =20 0   F    F  1.26D-01***********33.37558495 = 0.00356823 0.00030098  -61.8162325 ----
I have minimised the structure in = Amber7.0=20 before doing the calculation.
 
I think, the calculation is failing in = the Micro=20 Iteration.
 
But why it is not failing in the = Electronic=20 Emedding and what is the suitable solution for this.
 
 
Thanks in Advance,
 
Regards,
Mahesh S
 
 
 
------=_NextPart_000_0005_01C557F3.E7F21A80-- From chemistry-request@ccl.net Fri May 13 19:07:06 2005 Received: from mail.iinet.net.au (mail-04.iinet.net.au [203.59.3.36]) by server.ccl.net (8.13.1/8.13.1) with SMTP id j4DN6vwI021801 for ; Fri, 13 May 2005 19:06:59 -0400 Received: (qmail 15062 invoked from network); 13 May 2005 21:59:24 -0000 Received: from unknown (HELO octa4.net.au) (203.166.235.183) by mail.iinet.net.au with SMTP; 13 May 2005 21:59:23 -0000 Received: by octa4.net.au (sSMTP sendmail emulation); Sat, 14 May 2005 07:58:03 +0930 Date: Sat, 14 May 2005 07:58:03 +0930 From: Brian Salter-Duke To: chemistry=at=ccl.net Subject: Re: CCL:Comp.Chem. and Latin Message-ID: <20050513222802.GA3893=at=monster.octa4.net> Reply-To: Brian Salter-Duke Mail-Followup-To: chemistry=at=ccl.net References: <33831.131.188.174.179.1116000164.squirrel=at=wwwmail.chemie.uni-erlangen.de> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <33831.131.188.174.179.1116000164.squirrel=at=wwwmail.chemie.uni-erlangen.de> User-Agent: Mutt/1.5.4i X-Spam-Status: No, score=0.0 required=5.0 tests=none autolearn=failed version=3.0.3 X-Spam-Checker-Version: SpamAssassin 3.0.3 (2005-04-27) on server.ccl.net On Fri, May 13, 2005 at 06:02:44PM +0200, Anselm.Horn=at=chemie.uni-erlangen.de wrote: > Dear all, > > first my apologies for this slightly off topic question. > > I wonder whether there exists a Latin dictionary or established Latin > vocabulary for computer chemistry topics. > Of course, the Vatican does not deal with such things, and to the best of > my knowledge no comp.-chem. journal accepts articles in Latin; therefore > I'm rather convinced that there does not exist any 'official' word list > for quantum mechanics, force fields etc. (although most of the technical > terms have Latin roots), simply because Latin is not used. > However, I'd like to learn other people's opinion about that. Many years ago, the journal "Theoretica Chimica Acta" (now called Theoretical Chemistry Accounts) did allow papers in Latin (or in English, French or German and an insistence that all these three had to be used for the abstract). To my knowledge only one paper was ever published in Latin. It was written by Tony Whitehead and a colleague > from McGill University in Canada. I do not recall that TCA gave any assistance to anyone wanting to write a paper in Latin. You were on your own! Regards, Brian Duke. > Best regards, > > Anselm Horn > > > > > -= 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 is mail bouncing from ccl.net domain due to spam filters, please > use the Web based form from CCL Home Page > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > -- Brian Salter-Duke (Brian Duke) b_duke=at=octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/