From chemistry-request@server.ccl.net Sun Apr 13 08:08:16 2003 Received: from smtp4.dti.ne.jp ([202.216.228.39]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3DC8E318143 for ; Sun, 13 Apr 2003 08:08:15 -0400 Received: from oemcomputer (PPP174.fukuoka-ip.dti.ne.jp [211.132.92.174]) by smtp4.dti.ne.jp (3.08s) with SMTP id h3DC86iT017166 for ; Sun, 13 Apr 2003 21:08:10 +0900 (JST) Message-ID: <001601c301b4$d8ef2c40$ae5c84d3@oemcomputer> From: "Telkuni" To: Subject: Gaussian98W's IOp list (summary) Date: Sun, 13 Apr 2003 21:04:33 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" 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 Hello, CCLers I've sent a request: > Does anyone have Gaussian98W's IOp list? (I'm using > verA.7) > > I always utilize Gaussian's IOp page > http://www.gaussian.com/iops.htm , but it is not > available now. > > The IOp functions which I especially like to know > are . . . . . . . . Then I've recieved five replies. Here are three replies. Other have attached files. Thanks a lot! /// 1) from Faza Olalla Nieto ///// If you connect to the gaussian page (http://www.gaussian.com/tech_top_level.htm) you can download a zip file with the manual pages of g98 where you will be able to find the information you request. Hope it is useful. Regards Olalla Nieto Faza Dpto. Quimica Organica Universidade de Vigo Lagoas-Marcosende 36200 Vigo (Spain) e-mail: faza@uvigo.es /// 2) from Paul Davis ///// Go to this archive:- http://web.archive.org/web/20010802042313/www.gaussian.com/techinfo.htm -Paul -- -------------------------------------------------- Paul Davis paul@pdchem.demon.co.uk //// 3) from Roma Oakes ///// Thank you for the Word file. //// 4) from Alessandro Contini ///// Thank you for the PDF file. //// 5) from Michele Lunelli ///// There is a mirror of the old gaussian site, http://www.lct.jussieu.fr/manuals/Programmes/Gaussian98/index.htm and the IOps are at http://www.lct.jussieu.fr/manuals/Programmes/Gaussian98/iops.htm Best Regards, Michele Thank you ---------------------------------------------------- Telkuni Tsuru telkuni@venus.dti.ne.jp From chemistry-request@server.ccl.net Sun Apr 13 09:37:14 2003 Received: from oz.che.rochester.edu ([128.151.211.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3DDbE319301 for ; Sun, 13 Apr 2003 09:37:14 -0400 Received: (from janeou@localhost) by oz.che.rochester.edu (8.11.6+Sun/8.11.6) id h3DDc5b18674 for chemistry@ccl.net; Sun, 13 Apr 2003 09:38:05 -0400 (EDT) Date: Sun, 13 Apr 2003 09:38:05 -0400 (EDT) From: Jane-Jane Ou Message-Id: <200304131338.h3DDc5b18674@oz.che.rochester.edu> To: chemistry@ccl.net Subject: Frequency job with Gaussian98 Hello, again; I am currently running a frequency job with Gaussian98 after optimization. The optimization job did not take very long, however, the frequency job is going very slowly with warnings: **** Warning!!: The largest alpha MO coefficient is 0.10268903D+02 **** Warning!!: The smallest alpha delta epsilon is 0.84363472D-01 What do these warnings mean? Thanks in advancd. Sincerely, Jane Ou From chemistry-request@server.ccl.net Sun Apr 13 10:58:36 2003 Received: from antivirus1.its.rochester.edu ([128.151.57.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3DEwa320115 for ; Sun, 13 Apr 2003 10:58:36 -0400 Received: from antivirus1.its.rochester.edu (localhost [127.0.0.1]) by antivirus1.its.rochester.edu (8.12.9/8.12.4) with ESMTP id h3DEwaHs004427 for ; Sun, 13 Apr 2003 10:58:36 -0400 (EDT) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus1.its.rochester.edu (8.12.9/8.12.4) with SMTP id h3DEwZ2b004422 for ; Sun, 13 Apr 2003 10:58:35 -0400 (EDT) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.9/8.12.1) with ESMTP id h3DEwXt4028331 for ; Sun, 13 Apr 2003 10:58:33 -0400 (EDT) Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz@mail.rochester.edu Organization: university of rochester To: chemistry@ccl.net Subject: summary of DMSO charmm parameters Date: Sun, 13 Apr 2003 10:55:37 -0400 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200304131055.37708.weiz@mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h3DEwa320116 Hi, all: following are my original mail and the replies: ************************************** ORIGINAL **************************** >Hi, guys: > >I want to do a simulation of a peptide in DMSO. Can anybody point me to >some paper about the parameters of DMSO which I can use? thanks a lot. > >best regards >Wei Zhuang *************************************** REPLY 1 FROM Scott Feller ************************************* M.L. Strader and S.E. Feller, "A Flexible All-atom Model of Dimethylsulfoxide for Molecular Dynamics Simulations", J. Phys. Chem. A, 106, 1074-1080 (2002). ************************************** REPLY2 FROM Hannes Loeffler **************************************** Strader and Feller, J. Phys. Chem. A 106 (2002), 1074 ************************************** REPLY3 FROM Jeff Nauss" ******************************** You may look at: Strader ML, Feller SE. 2002. A Flexible All-Atom Model of Dimethyl Sulfoxide for Molecular Dynamics Simulations. J Phys Chem A 106: 1074 Mihailescu D, Smith JC. 1999. Molecular dynamics simulation of the cyclic decapeptide antibiotic, gramicidin S, in dimethyl sulfoxide solution. J Phys Chem B 103: 1586 Two different models. Jeff ************************************** REPLY4 FROM "C. Michael McCallum" ********************************* Hi Wei, Check out Krzysztof's site: http://pekoe.chem.ukans.edu/~kuczera/Public/web/html/charmm/proc/ proc.html It has a fairly detailed tutorial utilizing DMSO. Cheers, Mike *********************************************** REPLY 5 "Ya-Jun Zheng" ************************************ The AMBER-type DMSO parameters used in the following paper could be adopted in your CHARmm simulations: A molecular dynamics and quantum mechanics analysis of the effect of DMSO on enzyme structure and dynamics: substilisin, Zheng, Y. -J.; Ornstein, R. L.. J. Am. Chem. Soc. 1996, 118, 4175-4180. Yajun From chemistry-request@server.ccl.net Sat Apr 12 20:31:05 2003 Received: from oz.che.rochester.edu ([128.151.211.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3D0V5322852 for ; Sat, 12 Apr 2003 20:31:05 -0400 Received: from hra (vpn1-16.utd.rochester.edu [128.151.103.16]) by oz.che.rochester.edu (8.11.6+Sun/8.11.6) with SMTP id h3D0VtE29601 for ; Sat, 12 Apr 2003 20:31:55 -0400 (EDT) Message-ID: <004401c30153$5d4f5760$6601a8c0@rochester.rr.com> From: "Jane-Jane Ou" To: Subject: Freguency job with Gaussian98 Date: Sat, 12 Apr 2003 20:26:21 -0400 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Hello, again; I am currently running a frequency job with Gaussian98 after optimization. The optimization job did not take very long, however, the frequency job is going very slowly with a warning: **** Warning!!: The smallest alpha delta epsilon is 0.85685926D-01 What does this warning mean? Thank you ahead. Sincerely, Jane Ou From chemistry-request@server.ccl.net Sat Apr 12 12:42:47 2003 Received: from web21103.mail.yahoo.com ([216.136.227.105]) by server.ccl.net (8.11.6/8.11.0) with SMTP id h3CGgk318524 for ; Sat, 12 Apr 2003 12:42:46 -0400 Message-ID: <20030412164241.68033.qmail@web21103.mail.yahoo.com> Received: from [193.205.213.88] by web21103.mail.yahoo.com via HTTP; Sat, 12 Apr 2003 18:42:41 CEST Date: Sat, 12 Apr 2003 18:42:41 +0200 (CEST) From: =?iso-8859-1?q?Michele=20Lunelli?= Subject: Re: Gaussian98W's IOp list To: Telkuni Cc: CHEMISTRY@ccl.net In-Reply-To: <000b01c3001e$facd8e20$195c84d3@oemcomputer> MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit There is a mirror of the old gaussian site, http://www.lct.jussieu.fr/manuals/Programmes/Gaussian98/index.htm and the IOps are at http://www.lct.jussieu.fr/manuals/Programmes/Gaussian98/iops.htm Best Regards, Michele --- Telkuni ha scritto: > Hello, CCLers. > > Does anyone have Gaussian98W's IOp list? (I'm using > verA.7) > > I always utilize Gaussian's IOp page > http://www.gaussian.com/iops.htm , but it is not > available now. > > The IOp functions which I especially like to know > are > 30=1/8; > 8/6=1,10=1,23=2,27=262144000/1; > 9/27=262144000,41=6,42=1,48=2/14; . > > (These are concerning the TDDFT.) > > >...Any responses I'll appreciate and summarize > them. > > > Thanks in advance. > ---------------------------------------------------- > Telkuni Tsuru telkuni@venus.dti.ne.jp > > ______________________________________________________________________ Yahoo! Cellulari: loghi, suonerie, picture message per il tuo telefonino http://it.yahoo.com/mail_it/foot/?http://it.mobile.yahoo.com/index2002.html From chemistry-request@server.ccl.net Sun Apr 13 12:37:46 2003 Received: from antivirus1.its.rochester.edu ([128.151.57.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h3DGbk321471 for ; Sun, 13 Apr 2003 12:37:46 -0400 Received: from antivirus1.its.rochester.edu (localhost [127.0.0.1]) by antivirus1.its.rochester.edu (8.12.9/8.12.4) with ESMTP id h3DGbkHs018362 for ; Sun, 13 Apr 2003 12:37:46 -0400 (EDT) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus1.its.rochester.edu (8.12.9/8.12.4) with SMTP id h3DGbk2b018359 for ; Sun, 13 Apr 2003 12:37:46 -0400 (EDT) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.9/8.12.1) with ESMTP id h3DGbit4009742 for ; Sun, 13 Apr 2003 12:37:44 -0400 (EDT) Content-Type: text/plain; charset="iso-8859-1" From: wei Reply-To: weiz@mail.rochester.edu Organization: university of rochester To: chemistry@ccl.net Subject: a general question about simulation Date: Sun, 13 Apr 2003 12:34:48 -0400 User-Agent: KMail/1.4.1 References: <89C509BF71384142BCC18D3D0C4D4CEB3B2806@EXCHVS1.cs.cornell.edu> In-Reply-To: <89C509BF71384142BCC18D3D0C4D4CEB3B2806@EXCHVS1.cs.cornell.edu> MIME-Version: 1.0 Message-Id: <200304131234.48270.weiz@mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h3DGbk321472 Dear All: I have a general question about the peptide simulation, would anyone kindly give me some help about this? I read in many papers that when people do the simulation, they usually minimized the peptide in vacuum, then plug it in the solvent, then they fix the peptide and minimize the solvent to release the constraint. my question is why we need to fix the peptide at this step. is it better that we simply minimize the whole system? Wei