From chemistry-request@server.ccl.net Sat Feb 24 01:10:49 2001 Received: from gandalf.cber.nih.gov (gandalf.cber.nih.gov [128.231.52.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1O6Anw06294 for ; Sat, 24 Feb 2001 01:10:49 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id BAA26468; Sat, 24 Feb 2001 01:05:37 -0500 (EST) Date: Sat, 24 Feb 2001 01:05:37 -0500 From: Rick Venable To: "Claudio Redaelli (CSCS)" cc: CHEMISTRY@ccl.net Subject: Re: CCL:CHARMM In-Reply-To: <3A8B940A.67A5E7DE@cscs.ch> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 15 Feb 2001, Claudio Redaelli (CSCS) wrote: > Can you please send me the information about the right way to obtain > the source code of the CHARMM program? > > I'm trying to contact the CHARMM Development Project at Harvard > University > both by e-mail and by fax, with no response! The only method known to work is that recommended below: ----- blurb excerpt from http://yuri.harvard.edu/ ----- For-profit companies should contact Molecular Simulations Inc. Below is the standard reply to inquiries for the CHARMM program. We distribute the source code of the CHARMM program with documentation to individual academic research groups for a $600 licensing fee. CHARMM runs on a variety of UNIX workstations, including the SG Indigo machines. No graphics are necessary. The present version of the program being distributed is C27. The license is issued to the head of a laboratory or research group. Please send a letter with the full name and title of the professor in charge of your group and formal mailing address. Describe briefly the kind of research for which you intend to use the CHARMM program and the computers you will be using. The letter should be addressed to: The CHARMM Development Project Professor Martin Karplus Department of Chemistry & Chemical Biology 12 Oxford Street Harvard University Cambridge, Massachusetts 02138 ------ end excerpt ------ =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable@nih.gov ALT email: rvenable@speakeasy.org =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@server.ccl.net Sat Feb 24 04:22:36 2001 Received: from fep19-svc.tin.it (pop09-acc.tin.it [212.216.176.72]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1O9Maw06954 for ; Sat, 24 Feb 2001 04:22:36 -0500 Received: from powerpc ([212.171.84.27]) by fep19-svc.tin.it (InterMail vM.4.01.03.13 201-229-121-113) with SMTP id <20010224092040.CGMN19936.fep19-svc.tin.it@powerpc> for ; Sat, 24 Feb 2001 10:20:40 +0100 Message-ID: <003e01c09e43$815431f0$1b54abd4@powerpc> From: "Elisa Anzelmo" To: "CCL" Subject: atoms with no partial charge in pdb files Date: Sat, 24 Feb 2001 10:07:40 +0100 Hi, I'm optimizing some proteins (1ido.pdb, zoop.pdb, etc), coming from0 the Protein Data Bank, with Hyperchem 6.01. I've noticed that when I assign the partial charges by Amber96 the atoms belongin' to the last 10 residues of every protein are not charged. Can anybody explain me if there is a physics reason for this, or if I've some problem in the converting procedure (PDB to ENT file)? Thanks in advance, Elisa. From chemistry-request@server.ccl.net Sat Feb 24 16:50:56 2001 Received: from web12709.mail.yahoo.com (web12709.mail.yahoo.com [216.136.174.56]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f1OLouw10077 for ; Sat, 24 Feb 2001 16:50:56 -0500 Message-ID: <20010224215102.46678.qmail@web12709.mail.yahoo.com> Received: from [65.6.48.45] by web12709.mail.yahoo.com; Sat, 24 Feb 2001 13:51:02 PST Date: Sat, 24 Feb 2001 13:51:02 -0800 (PST) From: water Miller Subject: solvation model for simulation of macromolecule To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello everyone, I am very new to the field, hope someone could provide help, suggestion or comments. thanks a lot! In reference, there are about 3 kinds of models: (1)Discrete model: Most or all solvent molecules explicitly interact with solute in MM force field, but too expensive for computation. My question: as the development of computation hardware and software9algorithum), it this still a problem? At least, I have seen a lot of papers using this approach, eg. QM/MM. (2)Continum model: the solvent is treated as a dielectric continuum, providing a "reaction field". The solute and solvent polarizes each other. the most advantageof this model is cheap for computing, but it neglects the specific interactions between solvent and solute. My question: is this a serious problem? will the dynamics by this approach be very different from discrete model? (3)hybrid models: two-layer: discrete/QM for a few (1st shell) solvent + continuum/MM three-layer: discrete/QM for 1st shell solvent + 2nd layer solvent(explicit)/MM + continnum/MM My question: is this easy to implement for a dynamics simulation, MC or MD? My personal impression from some papers: the discrete model is more popular, and easy to implement, also usually gives good results(compared with experiments). is there any comment? Thanks a lot in advance! Water __________________________________________________ Do You Yahoo!? Get email at your own domain with Yahoo! Mail. http://personal.mail.yahoo.com/