From chemistry-request@server.ccl.net Thu Nov 2 08:34:38 2000 Received: from bif12.creighton.edu (bif12.creighton.edu [147.134.137.212]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA05131 for ; Thu, 2 Nov 2000 08:34:37 -0500 Received: from localhost (crwatts@localhost) by bif12.creighton.edu (8.9.3/8.9.3) with ESMTP id GAA15351 for ; Thu, 2 Nov 2000 06:29:11 -0600 Date: Thu, 2 Nov 2000 06:29:11 -0600 (CST) From: "Charles R. Watts" To: Computational Chemistry List Subject: Free energy calculations Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL: I have used molecular dynamics to sample the conformational space of a peptide in solution. The sampled conformations were then clustered into separate families of related conformations based on a pairwise comparison of the RMSD of all conformations. I would like to perform a free energy analysis that compares the separate families of conformations, hopefully in such a way that the solute and solvent terms could be analyzed separately.for simplicities sake I would like to do this using a representative conformation from each separate family.what would be the most appropriate, valid method and would a free energy perturbation calculate that mutates on conformation to the other be a valid choice? Your opinions would be greatly appreciated. Regards, Charles R. Watts, M.D., Ph.D. ************************************ Research Consultant * * Department of Biomedical Sciences * An appeaser is one who feeds * Creighton University * a crocodile, hoping it will eat * School of Medicine * him last. * 2500 California Plaza * * Omaha, NE 68178 * -Winston Churchill * phone: (402) 280-4042 * * Fax: (402) 553-8841 * * E-Mail: crwatts@bif12.creighton.edu ************************************ From chemistry-request@server.ccl.net Thu Nov 2 11:25:02 2000 Received: from www1.pobox.sk (www1.pobox.sk [212.5.216.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA05821 for ; Thu, 2 Nov 2000 11:25:01 -0500 Received: from www1.pobox.sk (www1.pobox.sk [212.5.216.11]) by www1.pobox.sk (8.9.3/8.9.3) with SMTP id RAA02779 for ; Thu, 2 Nov 2000 17:24:47 +0100 Date: Thu, 2 Nov 2000 17:24:47 +0100 Message-Id: <200011021624.RAA02779@www1.pobox.sk> From: Shotgun Reply-To: Shotgun Subject: Problems with IRC calculations To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=iso-8859-2 X-Pobox-Id: 672187806 X-User-Agent: Mozilla/4.0 (compatible; MSIE 5.5; Windows 98) X-Mailer: POBOX (mico's engine 5.0/3.0.1) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id LAA05822 Hi, I have a problem with some TS's and mostly IRC calculations.I have found transition state with only one imaginary frequency,visualisation shows it could by the correct TS, but IRC calculations lead in both directions to the same final structures with the same value of energy.Please help me with some advice or tricks ,that will solve this problem.Thank you. From chemistry-request@server.ccl.net Thu Nov 2 18:36:08 2000 Received: from ce.fis.unam.mx (ce.fis.unam.mx [132.248.33.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA07692 for ; Thu, 2 Nov 2000 18:36:07 -0500 Received: (from ramon@localhost) by ce.fis.unam.mx (8.9.3/8.9.3) id RAA27040 for chemistry@ccl.net; Thu, 2 Nov 2000 17:36:25 -0800 (PST) From: Ramon Garduno Message-Id: <200011030136.RAA27040@ce.fis.unam.mx> Subject: Difficulties using Discover of Biosym To: chemistry@ccl.net (CCL POST MSG) Date: Thu, 02 Nov 2000 17:36:25 PST X-Mailer: Elm [revision: 212.2] Dear CCLers: I have a problem running a Discover job (BIOSYM-InsightII 95) that I have been dealing with for about one week, and finally I have given up. I would like to hear from more advanced users of this software. I am sure that the system I want to study does not represent a problem since many other researchers have used it for larger molecules. This is what I have done... 1) Built a system of one cyclodextrin molecule (146 atoms) and a ibuprofen molecule (32 atoms) soaked with 2040 water molecules. 2) This system is held in a cubic box of 40 angstrom per side 3) I have selected the PCB option and the amber force field. 4) I have set cutoff = 19.0 cutdis =18.0 and swtdis = 1.5. 5) The current limits are total no. atoms 6285 limit 25000 total no. groups 2037 limit 8000 total no. residues 2037 limit 7520 total no. molecules 2037 limit 7500 total no. bonds 4257 limit 30000 total no. valence angles 2380 limit 50000 total no. torsion angles 542 limit 75000 total no. out of planes 7 limit 7500 total no. theta*theta angles 0 limit 87500 total no. excluded atoms 14310 limit 325000 However I get these errors which I do not understand....... error : too many atoms generated for dimensions change MXATM to exceed the number of atoms generated error : too many groups generated for dimensions change MXGRP to exceed the number of groups generated error: dimensions for groups must be at least 10125 Discover must halt. error: dimensions for atoms must be at least 25302 Discover must halt. I will appreciate any hints as to how I can fix my problem. Much obliged, Ramon -- "There are so many ways.... There is so little time...." "Hay tantos caminos..... Pero, hay tan poco tiempo....." ___________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics CENTRO DE CIENCIAS FISICAS | EMAIL: ramon@ce.fis.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | Apdo. Postal 48-3 | VOICE: +52(5)6227749 ; +52(7)3291749 62251 Cuernavaca, Morelos | MEXICO | FAX: +52(5)6227775 & +52(7)3291775 ___________________________________EOF ____________________________________