From chemistry-request@server.ccl.net Mon Jun 25 01:12:57 2001 Received: from edda.vcp.monash.edu.au ([130.194.217.57]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5P5Cs503584 for ; Mon, 25 Jun 2001 01:12:55 -0400 Received: from localhost (david@localhost) by edda.vcp.monash.edu.au (SGI-8.9.3/8.9.3) with ESMTP id PAA27905 for ; Mon, 25 Jun 2001 15:16:14 +1000 (EST) X-Authentication-Warning: edda.vcp.monash.edu.au: david owned process doing -bs Date: Mon, 25 Jun 2001 15:16:13 +1000 From: David Chalmers X-Sender: To: Subject: Charmm MMFF in parallel? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All, I have asked this question on the beowulf list but I did not get a result > from there - so I will try the CCL list. I am trying to use the MMFF forcefield in Charmm on our Intel/Linux/Redhat 7.1 Cluster. This works well on a single processor but dies when I attempt to run the same job in parallel. Does anybody know if the MMFF forcefield is parallelised in Charmm? Regards, David _____________________________________________________________________________ David Chalmers Lab: 9903 9110 Victorian College of Pharmacy Fax: 9903 9582 381 Royal Pde, Parkville, Vic 3053 http://synapse.vcp.monash.edu.au Australia David.Chalmers@vcp.monash.edu.au _____________________________________________________________________________ From chemistry-request@server.ccl.net Mon Jun 25 09:21:43 2001 Received: from navarra.chemie.fu-berlin.de ([160.45.24.110]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5PDLg521980 for ; Mon, 25 Jun 2001 09:21:43 -0400 Received: from localhost (ahwagner@localhost) by navarra.chemie.fu-berlin.de (8.10.2/8.10.2/SuSE Linux 8.10.0-0.3) with ESMTP id f5PDLdM03398 for ; Mon, 25 Jun 2001 15:21:39 +0200 X-Authentication-Warning: navarra.chemie.fu-berlin.de: ahwagner owned process doing -bs Date: Mon, 25 Jun 2001 15:21:39 +0200 (CEST) From: Armin Wagner To: Subject: deformation density Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I'm looking for a program which can generate deformation densities from theoretical wavefunctions. This concept is originated in crystallography to generate a difference map of a "real" (experimental or theoretical) electron density and the density of a hypothetical promolecule (consisting of non deformated spherical atoms). The programs I know to do this job for theoretical wavefunctions are molden and an in-house solution which are both restricted to HF wavefunctions and rather low basis sets. Does anybody know other programs? Thanks, Armin *-----------------------------------------------------------------------------* | Armin Wagner ahwagner@chemie.fu-berlin.de | | www.chemie.fu-berlin.de/~ahwagner | | Freie Universitaet Berlin | | Institut fuer Kristallographie, R 111 | | Takustr. 6 Tel.: 030/838-52354 | | 14195 Berlin Fax: 030/838-53464 | *-----------------------------------------------------------------------------* From chemistry-request@server.ccl.net Mon Jun 25 14:43:51 2001 Received: from post2.inre.asu.edu ([129.219.110.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5PIhp526460 for ; Mon, 25 Jun 2001 14:43:51 -0400 Received: from conversion.post2.inre.asu.edu by asu.edu (PMDF V6.0-24 #47347) id <0GFI00H011D2EF@asu.edu> for chemistry@ccl.net; Mon, 25 Jun 2001 11:43:50 -0700 (MST) Received: from webmail1.asu.edu (webmail1.asu.edu [129.219.10.21]) by asu.edu (PMDF V6.0-24 #47347) with ESMTP id <0GFI00DQT1D2I4@asu.edu>; Mon, 25 Jun 2001 11:43:50 -0700 (MST) Received: (from nobody@localhost) by webmail1.asu.edu (8.9.3/8.9.3) id LAA10629; Mon, 25 Jun 2001 11:43:50 -0700 Date: Mon, 25 Jun 2001 11:43:50 -0700 (MST) From: Benjamin.Moritz@asu.edu Subject: Freqchk X-Originating-IP: 149.169.26.88 To: chemistry@ccl.net, help@gaussian.com Message-id: <993494630.3b378666dd436@webmail1.asu.edu> MIME-version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.3 Dear All, I'm trying to perform some freq calculations of an adsorbed species on a copper complex and want to set the mass of the copper to a large mass (say 1000). When I employ the freqchk command and try to set the value of the copper atom to 1000 I get an error saying that the only known masses for the copper are 62 and 64. How do I get G98 to calculate the frequencies so that the copper is 1000? Also I want to view the frequencies of the new "frozen" species using MOLEKEL. How do I import the data of the "frozen" frequencies into MOLEKEl so I can view them? Thank you in advance for any suggestions. ******************************************************************************** Benjamin J. Moritz Work: 480-965-8509 College of Engineering and Applied Sciences Mailto:bmoritz@asu.edu Dept. of Chemical & Materials Engineering PO Box 876006 Tempe, AZ 85287-6006 ******************************************************************************** From chemistry-request@server.ccl.net Mon Jun 25 15:28:48 2001 Received: from mail.chem.tamu.edu (IDENT:root@[165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5PJSm527074 for ; Mon, 25 Jun 2001 15:28:48 -0400 Received: from [165.91.177.32] (account yubofan HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.4.7) with ESMTP id 76612 for CHEMISTRY@ccl.net; Mon, 25 Jun 2001 14:26:54 -0500 Sender: yubo@ccl.net Message-ID: <3B3790F2.9C2EDDA4@mail.chem.tamu.edu> Date: Mon, 25 Jun 2001 14:28:51 -0500 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Compiling G98 on Linux Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id f5PJSm527075 Hi, everyone, We met problems on compiling G98 on RedHat Linux 7.1. Could you please tell me the detailed procedure? Where should we put the BLAS library? Thanks in advance Yubo -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ From chemistry-request@server.ccl.net Mon Jun 25 05:12:56 2001 Received: from mail.shcnc.ac.cn ([202.127.16.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5P9Cs516058 for ; Mon, 25 Jun 2001 05:12:54 -0400 Received: from PC18 ([202.127.19.225]) by mail.shcnc.ac.cn (8.9.3/8.9.3) with SMTP id RAA04598 for ; Mon, 25 Jun 2001 17:11:50 +0800 (CDT) Message-Id: <200106250911.RAA04598@mail.shcnc.ac.cn> Date: Mon, 25 Jun 2001 17:6:59 +0800 From: bxiong To: "chemistry@ccl.net" Subject: X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Dear Members: because my residue in the protein is a non-normal amino acid ,so the AMBER can not recognize it .I want to fit the charge . but I can not determine what structure I use? Is I use the whole residue which have the normal COOH and NH2 or I use the structure which deleted OH and H(NH2) ? Can anyone give me suggestion about how to calculate charge of it ? thanks!!! Best regards! bxiong@mail.shcnc.ac.cn Xiong Bin Shanghai Institute of Materia Medica, C.A.S. phone:021-64311833-222(office) From chemistry-request@server.ccl.net Sun Jun 24 21:00:52 2001 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5P10q502070 for ; Sun, 24 Jun 2001 21:00:52 -0400 Received: from eyou.com ([61.136.62.73]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with SMTP id VAA10252 for ; Sun, 24 Jun 2001 21:00:49 -0400 (EDT) Received: (qmail 26324 invoked from network); 25 Jun 2001 09:00:48 +0800 Received: from unknown (HELO eyou.com) (172.16.2.1) by 172.16.1.1 with SMTP; 25 Jun 2001 09:00:48 +0800 Received: (qmail 26195 invoked by uid 65534); 25 Jun 2001 09:00:48 +0800 Date: 25 Jun 2001 09:00:48 +0800 Message-ID: <20010625090048.26194.qmail@eyou.com> From: "王明韬" To: CHEMISTRY@ccl.net Reply-To: "王明韬" Subject: help Dear all: How can i treat heteroatoms,such as metal ion Co(II),when i carry out the molecular minimization or dynamic simulation using Discover? To speak specificly,how can i assign charges and potentials to these heteroatoms? Thanks! Yours, 25/6/2001 --http://www.eyou.com --稳定可靠的免费电子信箱 语音邮件 移动书签 日历服务 网络存储...亿邮未尽 From chemistry-request@server.ccl.net Mon Jun 25 05:33:01 2001 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5P9X0526541 for ; Mon, 25 Jun 2001 05:33:01 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id LAA08853 ; Mon, 25 Jun 2001 11:32:56 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id LAA13582; Mon, 25 Jun 2001 11:31:22 +0200 Date: Mon, 25 Jun 2001 11:31:22 +0200 Message-Id: <200106250931.LAA13582@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: mike_smith07@yahoo.com CC: chemistry@ccl.net In-reply-to: <20010623034814.60996.qmail@web13208.mail.yahoo.com> (message from mike smith on Fri, 22 Jun 2001 20:48:14 -0700 (PDT)) Subject: Re: CCL:MD package for arbitary model and force field? References: <20010623034814.60996.qmail@web13208.mail.yahoo.com> > I am looking for some kind of general MD package, > which > can be used for ARBITARY model and force field. Have a look at the Molecular Modelling Toolkit: http://dirac.cnrs-orleans.fr/MMTK/ Being Open Source, it allows users to modify whatever they wish. And it is even designed to make modifications and enhancements easy to implement. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais -------------------------------------------------------------------------------