From chemistry-request@server.ccl.net Mon Nov 25 01:26:48 2002 Received: from hotmail.com ([207.68.165.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAP6QmO16052 for ; Mon, 25 Nov 2002 01:26:48 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Sun, 24 Nov 2002 22:26:48 -0800 Received: from 137.189.4.4 by sea2fd.sea2.hotmail.msn.com with HTTP; Mon, 25 Nov 2002 06:26:47 GMT X-Originating-IP: [137.189.4.4] From: "Ma Dicky" To: chemistry@ccl.net Subject: About the charge schemes used in gaussian98 for calculation. Date: Mon, 25 Nov 2002 06:26:47 +0000 Mime-Version: 1.0 Content-Type: text/plain; charset=big5; format=flowed Message-ID: X-OriginalArrivalTime: 25 Nov 2002 06:26:48.0145 (UTC) FILETIME=[A2046410:01C2944B] To Dear All: My name is Dicky, who is a student of Chinese University of Hong Kong. I have some questions about the charge schemes used in calculation in gaussian98 that i still make it not clear. I have run a trial before my formal calculation. After that i compare the 'four' charge assigning methods, that are NPA in NBO, chelpg, chelp and mk methods. It is quite strange that the result are not consistent! For example, some atoms under NPA show positive values in charges but while in other methods they show negative values! So i want to ask, Among these methods, which one is the best or which is better in assigning the charges for large molecules(such as protein or DNA)?? Also any evidence supports the choice of the charge schemes?? I really appreciate of your help. Thanks a lot!! Best regards, Dicky _________________________________________________________________ 在您的行動裝置上傳送接收 Hotmail 郵件，請移至: http://zh-asiasms.mobile.msn.com From chemistry-request@server.ccl.net Sun Nov 24 19:53:11 2002 Received: from antivirus2.its.rochester.edu ([128.151.57.53]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAP0rAO08391 for ; Sun, 24 Nov 2002 19:53:10 -0500 Received: from antivirus2.its.rochester.edu (localhost [127.0.0.1]) by antivirus2.its.rochester.edu (8.12.4/8.12.4) with ESMTP id gAP0r08a015702 for ; Sun, 24 Nov 2002 19:53:00 -0500 (EST) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus2.its.rochester.edu (8.12.4/8.12.4) with SMTP id gAP0qoDj015676 for ; Sun, 24 Nov 2002 19:52:50 -0500 (EST) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.4/8.12.1) with ESMTP id gAP0qnkk023096 for ; Sun, 24 Nov 2002 19:52:49 -0500 (EST) Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz@mail.rochester.edu Organization: university of rochester To: chemistry@ccl.net Subject: help about NAMD Date: Sun, 24 Nov 2002 19:51:25 -0500 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200211241951.25609.weiz@mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id gAP0rBO08392 Hi,all: Does any body know how to do NPT simulation using NAMD?there is no keyword to specify what ensemble to choose. does it mean that I only need to set the "temperature coupling parameters" and "pressure bath coupling parameters"? wei zhuang department of chemistry university of rochester From chemistry-request@server.ccl.net Mon Nov 25 05:59:40 2002 Received: from betty.virtex.it ([194.243.91.42]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gAPAxdO27536 for ; Mon, 25 Nov 2002 05:59:39 -0500 Received: (qmail 16873 invoked by uid 99); 25 Nov 2002 10:59:38 -0000 Message-ID: <20021125105938.16872.qmail@betty.virtex.it> To: Subject: cation-pi interaction Reply-To: Mark Ripley From: Mark Ripley Date: Mon, 25 Nov 2002 10:59:38 +0000 Organization: www.wappi.com by Movenda S.p.A. X-Mailer: PHP/3.0.18 X-Scripts-by: sergio@ascia.net X-Remote_Host: X-Remote_Addr: 192.167.124.8 X-User_Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.1b) Gecko/20020721 X-Forwarded_For: X-Via: Content-Transfer-Encoding: binary MIME-Version: 1.0 Content-Type: text/plain Dear CCLers, my studies concern molecular dynamics simulation of protein-protein complex where main interactions are of the cation-pi type. As far as I know common force fields like that of Amber are not able to 'handle' that interaction. Is anyone aware of force fields capable of dealing with cation-pi interaction? Thanks in advance, Mark. --- Mail inviata con il servizio WebMail di Wappi Connetti ad internet il tuo telefonino: http://www.wappi.com/ Wappi e' un servizio di Movenda S.p.A. http://www.movenda.com/ From chemistry-request@server.ccl.net Mon Nov 25 10:15:33 2002 Received: from maild.telia.com ([194.22.190.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAPFFWO03538 for ; Mon, 25 Nov 2002 10:15:32 -0500 Received: from d1o916.telia.com (d1o916.telia.com [213.65.164.241]) by maild.telia.com (8.12.5/8.12.5) with ESMTP id gAPFFWKd008384; Mon, 25 Nov 2002 16:15:32 +0100 (CET) X-Original-Recipient: chemistry@ccl.net Received: from [192.168.0.101] (h113n2fls32o916.telia.com [213.67.37.113]) by d1o916.telia.com (8.10.2/8.10.1) with ESMTP id gAPFFXi06106; Mon, 25 Nov 2002 16:15:34 +0100 (CET) Mime-Version: 1.0 X-Sender: u42123287@m1.421.telia.com (Unverified) Message-Id: In-Reply-To: <20021125105938.16872.qmail@betty.virtex.it> References: <20021125105938.16872.qmail@betty.virtex.it> Date: Mon, 25 Nov 2002 16:13:17 +0100 To: Mark Ripley From: Per-Ola Norrby Subject: Re: CCL:cation-pi interaction Cc: chemistry@ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" >Dear CCLers, > >my studies concern molecular dynamics simulation of protein-protein >complex where main interactions are of the cation-pi type. As far as >I know common force fields like that of Amber are not able to >'handle' that interaction. Is anyone aware of force fields capable >of dealing with cation-pi interaction? > >Thanks in advance, Mark. Dear Mark, We've looked a bit at ammonium-benzene interactions, mostly QM, but also some force field checks. In our experience, the interaction can be at least partially modelled by standard force fields, provided that the aromatic ring has a negatively charged core and positive hydrogens (as in Amber and MM3, but not standard MM2). With the force fields in MacroModel (among them Amber*), we find that roughly half the interaction energy is captured by the force field. I believe that Peter Kollman studied solvated cation-pi systems in some detail using AMBER, but I don't have the reference handy. Allinger added some terms for using sp2 carbons as hydrogen bond acceptors in MM3. Such a potential could capture the rest of the interaction, also for a benzene-M+ system, but not all programs allow you to add this potential. Some programs will only allow hydrogen bond potentials for heteroatom-hydrogen...heteroatom. Best, Per-Ola -- Per-Ola Norrby, Assoc. Professor, http://compchem.dfh.dk/PeO/ Technical University of Denmark, Deptartment of Chemistry Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon@kemi.dtu.dk tel +45-45252123, fax +45-45933968 From chemistry-request@server.ccl.net Mon Nov 25 13:35:06 2002 Received: from ChE.UDel.Edu ([128.175.117.64]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAPIZ6O11433 for ; Mon, 25 Nov 2002 13:35:06 -0500 Received: from chem.udel.edu (struppi.che.udel.edu [128.175.117.107]) by ChE.UDel.Edu (8.9.3/8.9.3) with ESMTP id NAA02725; Mon, 25 Nov 2002 13:35:06 -0500 (EST) Message-ID: <3DE26EBA.2000301@chem.udel.edu> Date: Mon, 25 Nov 2002 13:40:58 -0500 From: Stephen Garrison User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:0.9.4) Gecko/20011019 Netscape6/6.2 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net, help@gaussian.com Subject: MP2 Optimizations with G98 A.11 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Is there a way to force G98 to do an MP2 optimization using only the energies (i.e. a numerical optimization, e.g. the numerical eigenvalue following routine) instead of using analytical gradients? From chemistry-request@server.ccl.net Mon Nov 25 15:40:42 2002 Received: from gip2.u-picardie.fr ([193.49.184.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gAPKegO19551 for ; Mon, 25 Nov 2002 15:40:42 -0500 Received: by gip2.u-picardie.fr (Postfix, from userid 33) id 699A191E7; Mon, 25 Nov 2002 21:40:42 +0100 (CET) To: chemistry@ccl.net Subject: SCF convergence with Lanthanide ECP/Basis set Message-ID: <1038256842.3de28aca5d309@webmail.u-picardie.fr> Date: Mon, 25 Nov 2002 21:40:42 +0100 (CET) From: FyD MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.6 Dear All, I am using the Cundari & Stevens ECP with the corresponding BASIS SET to optimize some Lanthanide derivatives. The SCF procedure DOES converge but demands a looot of steps with GAMESS or Gaussian98 (close or more than 200; the convergence is very slow). Is it a known problem for such calculations (such molecules and particular ECP/basis sets) and is there a way to decrease this number of SCF steps ? As in GAMESS the maximum number of SCF step is 200 how could I do if the SCF demand more than these 200 steps ? Should I modify the GAMESS source code and should I recompile GAMESS ? Thanks, regards, Francois