From chemistry-request@ccl.net Mon Jun 23 19:53:29 2003 Received: from adenine.cgl.ucsf.edu (socrates.cgl.ucsf.edu [169.230.27.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5NNrS5u008215 for ; Mon, 23 Jun 2003 19:53:28 -0400 Received: from localhost (socrates.cgl.ucsf.edu [169.230.27.3]) by adenine.cgl.ucsf.edu (8.12.9/8.12.9/GSC1.16) with ESMTP id h5NNrSqa923846 for ; Mon, 23 Jun 2003 16:53:28 -0700 (PDT) Date: Mon, 23 Jun 2003 16:53:28 -0700 (PDT) From: Pradipta Bandyopadhyay To: chemistry/at/ccl.net Subject: superimposing two molecules!! Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Does anyone have a code (in fortran), which superimposes two molecules? I am looking for the implementation of the algorithm mentioned in the W. Kabsch paper (Acta. Crys.A 32, 922). thanks. Pradipta From chemistry-request@ccl.net Mon Jun 23 20:15:45 2003 Received: from hauptpostamt.charite.de (hauptpostamt.charite.de [193.175.66.220]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5O0Fi5u008689 for ; Mon, 23 Jun 2003 20:15:44 -0400 Received: from postamt1.charite.de (postamt1.charite.de [193.175.66.246]) by hauptpostamt.charite.de (Postfix) with ESMTP id 182E015C005; Tue, 24 Jun 2003 02:15:41 +0200 (CEST) Received: from linux (jsaam.max.charite.de [172.26.7.233]) by postamt1.charite.de (Postfix) with ESMTP id 9674B633B5; Tue, 24 Jun 2003 02:15:40 +0200 (CEST) Content-Type: text/plain; charset="iso-8859-15" From: Jan Saam Reply-To: jan.saam$at$charite.de To: Dominique Vlieghe , vmd-l$at$ks.uiuc.edu Subject: Re: Simple potential energy calculations in VMD Date: Tue, 24 Jun 2003 02:19:47 +0200 X-Mailer: KMail [version 1.4] Cc: chemistry$at$ccl.net References: <1056382485.17625.6.camel$at$LMB032.rug.ac.be> In-Reply-To: <1056382485.17625.6.camel$at$LMB032.rug.ac.be> MIME-Version: 1.0 Message-Id: <200306240219.48164.jan.saam$at$charite.de> X-Virus-Scanned: by amavisd-new at charite.de Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h5O0Fj5u008690 Dear Dominique, VMD cannot do this. Even though you could theoretically hook it to NAMD using the IMD interface and let NAMD calculate the energies. You only get total energies with this, though. But I once wrote a plugin that can calculate energies for and between atom selections. I haven't touched it for a while and need to dig it out again. It is easy to use, but I should write some documentation for it . Give me 2-3 days, then I'll post it. I also have to check with John first as the major part of the code is derived > from VMD and NAMD so that the software belongs to the Uniersity of Illinois. Therefore they must agree to the distribution. Have a little patience, Jan Am Montag, 23. Juni 2003 17:34 schrieb Dominique Vlieghe: > Hi all, > > Is it possible to do simple energy calculations within VMD (without > prior energy minimisations and/or dynamics). Furthermore, is it possible > to calculate energies between (atom) selections? > > Regards, > > Dominique From chemistry-request@ccl.net Tue Jun 24 09:07:33 2003 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h5OD7X5u026186 for ; Tue, 24 Jun 2003 09:07:33 -0400 Received: from email.unb.ca (root*at*newpop.unb.ca [131.202.3.46]) by mailserv.unb.ca (8.12.6/8.12.6) with ESMTP id h5OD7NXd028176 for ; Tue, 24 Jun 2003 10:07:24 -0300 Received: from [131.202.130.26] (HELO webmail1) by email.unb.ca (CommuniGate Pro SMTP 4.0.6) with ESMTP id 11691662 for chemistry*at*ccl.net; Tue, 24 Jun 2003 10:07:23 -0300 X-WebMail-UserID: l72k6 Date: Tue, 24 Jun 2003 10:07:23 -0300 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: CCL: local search in AutoDock Message-ID: <3EF8BB49@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 X-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: not spam (whitelisted), SpamAssassin (score=1.4, required 7, FROM_HAS_MIXED_NUMS, SPAM_PHRASE_03_05) Hi, I'm trying to use a local search (pseudo-sw) to minimize a docked pose of a ligand into a receptor. When I look at the ligand and the receptor in ADT, the ligand is in the correct starting position. The Grid box is large enough to contain the search space. I'm using a non-random start, non-random relative dihedral offset, and initial relative dihedrals, which should all start the local search from the specified initial coordinates. The output ligand poses end up completely outside the docking box, and outside the receptor as well, with an RMSD of 85 Angstroms!!! Can anyone tell me what is happening, as I see no reason why the ligand should end up outside the docking box! Thank you for your help, -Robert ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: robert.flight*at*unb.ca ******************************** "People think it must be fun to be a super genius, but they don't realize how hard it is to put up with all the idiots in the world." -Calvin from Calvin & Hobbes From chemistry-request@ccl.net Tue Jun 24 16:06:44 2003 Received: from salmon.maths.tcd.ie (salmon.maths.tcd.ie [134.226.81.11]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h5OK6h5u004429 for ; Tue, 24 Jun 2003 16:06:43 -0400 Received: from bell.maths.tcd.ie by salmon.maths.tcd.ie with SMTP id ; 24 Jun 2003 21:06:43 +0100 (BST) Date: Tue, 24 Jun 2003 21:06:42 +0100 (BST) From: Gemma Kinsella To: chemistry|at|ccl.net Subject: CCL: Charmm Cl parameters Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I have recently switched to the charmm force field from amber, and am interested in performing some simulations in CHCl3 and CCL4. Unfortunately I have been unable to find Cl parameters in Charmm and was wondering if such were available or if there is a methodology for converting from amber to charmm parameters! Many thanks, Gemma Kinsella