From lim@rani.chem.yale.edu Fri Feb 20 01:13:04 1998 Received: from rani.chem.yale.edu for lim@rani.chem.yale.edu by www.ccl.net (8.8.3/950822.1) id AAA25132; Fri, 20 Feb 1998 00:46:56 -0500 (EST) Received: by rani.chem.yale.edu; Fri, 20 Feb 98 00:46:57 -0500 From: Dongchul Lim Message-Id: <9802200546.AA22440@rani.chem.yale.edu> Subject: Organic Synthesis in the Cyber Space To: chemistry@www.ccl.net (Computational Chemistry) Date: Fri, 20 Feb 98 0:46:56 EST Dear chemists, CAMEO (Computer Assisted Mechanistic Evaluation Organic Reactions) is an organic synthesis software which runs on VAX/VMS, SGI, and Mac. Available reaction modules include Carbene, Basic/Nucleophilic, Acidic/Electrophilic, Electrophilic/Aromatic, Transition Organometallic, Free Radical, Heterocyclic, Oxidative/Reductive, Pericyclic, and Photocyclic reactions. We are now running an on-line interactive CAMEO server on our HTTP server. Check out the CAMEO home page at http://zarbi.chem.yale.edu/programs/cameo.html or you can directly connect to the server at http://zarbi.chem.yale.edu/~lim/CameoClient/index.html This client/server was written in JAVA 1.0 and thus requires JAVA enabled world wide web browsers such as netscape 4.0 or later. Within a web browser, you can draw starting materials and reactants, choose a desired reaction module and reaction conditions, and analyze products and reaction mechanisms. This service is provided for FREE for a limited period of time. --- Dongchul Lim, lim@rani.chem.yale.edu William L. Jorgensen Research Group Dept of Chemistry, Yale University From zhangxd@xx1.icas.ac.cn Fri Feb 20 04:13:07 1998 Received: from xx1.icas.ac.cn for zhangxd@xx1.icas.ac.cn by www.ccl.net (8.8.3/950822.1) id DAA26266; Fri, 20 Feb 1998 03:32:40 -0500 (EST) Received: (from zhangxd@localhost) by xx1.icas.ac.cn (8.6.12/8.6.9) id QAA04400; Fri, 20 Feb 1998 16:44:24 +0800 Date: Fri, 20 Feb 1998 16:44:23 +0800 (CST) From: zhang To: szilagyi@almos.vein.hu cc: Karl Irikura , chemistry@www.ccl.net Subject: calulation of oxidation potental In-Reply-To: <34E9B9DC.1CD8@mm2.vein.hu> Message-ID: Dear Netters Now I want to calculate the oxidation potental of macromolecules, such as polymer and protein etc with quantum chemical methods . Thanks in advances! Sincerly yours zhangxd From bjoerno@chem.uit.no Fri Feb 20 04:19:48 1998 Received: from kvikk.uit.no for bjoerno@chem.uit.no by www.ccl.net (8.8.3/950822.1) id EAA26406; Fri, 20 Feb 1998 04:09:17 -0500 (EST) Received: from james.chem.uit.no (james.Chem.Uit.No [129.242.24.111]) by kvikk.uit.no (8.8.8/8.8.8) with ESMTP id KAA23233 for ; Fri, 20 Feb 1998 10:09:17 +0100 (MET) Received: from blipp.chem.uit.no ([129.242.24.139]) by james.chem.uit.no (8.7.3/8.7.1) with SMTP id JAA16258; Fri, 20 Feb 1998 09:36:19 +0100 (MET) Received: by localhost with Microsoft MAPI; Fri, 20 Feb 1998 09:35:13 +0100 Message-ID: <01BD3DE2.D8106BE0.bjoerno@chem.uit.no> From: =?iso-8859-1?Q?Bj=F8rn_Olav_Brandsdal?= To: "'chemistry@www.ccl.net'" Cc: "'bjoerno@chem.uit.no'" Subject: CCL: Free Energy Perturbation Date: Fri, 20 Feb 1998 09:35:12 +0100 Hello, I am trying to perform a free energy perturbation/simulation of a protein-inhibitor complex using the academic version of CHARMM. I have had some problems when trying to create a proper input file for a mutation of an amino acid to another in the inhibitor. In the testcases distributed along with CHARMM, there was an example of an input file for perturbation, and I have used the punit file for this exapmle. However, it ony calculates the first line of this file, that it lambda 0.0 to 0.05, then the program terminates normally. This is the same for all mutations I have done when the number of atoms in the two residues to be mutated are the same. When the number of atoms are different in the lambda 0 and 1 state, dummy atoms must be defined, and there does not seem to an easy way of doing this in CHARMM. So I was wondering if anyone has an exapmle of an input file for free energy perturbation for CHARMM, and if somebody could tell me of how to add dummy atoms. Best regards, Bjoern O. Brandsdal Bjoern Olav Brandsdal Department of Chemistry University of Tromsoe 9037 Tromsoe, Norway Phone: +47-776-44063 Fax: +47-776-44765 E-mail: bjoerno@chem.uit.no From lavelle@mbi.ucla.edu Fri Feb 20 17:13:12 1998 Received: from theta1.ben2.ucla.edu for lavelle@mbi.ucla.edu by www.ccl.net (8.8.3/950822.1) id RAA01477; Fri, 20 Feb 1998 17:00:45 -0500 (EST) Received: from ewald.mbi.ucla.edu (ewald.mbi.ucla.edu [128.97.39.21]) by theta1.ben2.ucla.edu (8.8.8/8.8.8) with SMTP id OAA17570; Fri, 20 Feb 1998 14:00:47 -0800 Received: from red5.mbi.ucla.edu by ewald.mbi.ucla.edu (5.65v3.2/1.1.10.5/09Oct97-1217PM) id AA16982; Fri, 20 Feb 1998 14:00:46 -0800 Message-Id: <3.0.32.19980220141654.0098ea00@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Fri, 20 Feb 1998 14:16:54 -0800 To: "Dale A. Braden" , cclpost From: Laurence Lavelle Subject: Re: CCL:PC configuration for QM At 12:22 PM 2/20/98 -0800, Dale A. Braden wrote: >Dear CCL, > >I've looked at the CCL archives for info on this question, but the most >up-to-date advice is important. > >I'm going to set up a PC/Linux system for doing quantum chemical >calculations (probably using Q-Chem and Red Hat Linux 5.0), and the >question is, What sort of hardware should I buy? Rather than ask for >answers to this broad question, I'd like to suggest a system and solicit >criticisms of it. Here goes: > >I plan on getting a dual-cpu PentiumII 333Mhz motherboard (these have the >usual 512K L2 cache), 128Mb SDRAM, and two ultrawide SCSI drives (as large After the CPU, cache is the most important. Accept nothing less than 1MB per CPU. Digital did a demo here some months back and stated that CPU intensive jobs show exponential dependence on cache size for their CPU's (don't know the cutoffs). They have/will release their latest 600MHZ alpha's with 4MB cache modules per CPU as an option. I would expect 1M cache/CPU for your high end Intel. I have heard of intel motherboards taking up to 2MB cache/CPU. Bottom line is cache is very important for CPU intensive work. Laurence
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read.