From chemistry-request@server.ccl.net Fri May 2 07:48:26 2003 Received: from mail.nii.res.in ([202.54.102.178]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h42BmPV25250 for ; Fri, 2 May 2003 07:48:25 -0400 Received: from www.nii.res.in ([202.54.102.186] helo=nii.res.in) by mail.nii.res.in with smtp (Exim 3.36 #1) id 19BYbq-0004G0-00 for chemistry@server.ccl.net; Fri, 02 May 2003 16:51:46 +0530 Date: Fri, 02 May 2003 16:51:46 +0530 (IST) From: Gitanjali Yadav To: chemistry@server.ccl.net Subject: CCL:AMBER7/Cyclic Peptide X-Mailer: NII Webmail version v2.1 X-URL: http://mail.nii.res.in Message-Id: hi all How can one make required input files for simulation of a cyclic peptide in AMBER7. What I have is a starting coordinate for this peptide in PDB format. From chemistry-request@server.ccl.net Fri May 2 11:23:10 2003 Received: from ns1.scripps.edu ([192.42.82.59]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id h42FN8V25808 for ; Fri, 2 May 2003 11:23:08 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.7/TSRI-4.1rx) with SMTP id h42FN2p15600 for ; Fri, 2 May 2003 08:23:02 -0700 (PDT) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id 16135; Fri, 02 May 2003 08:21:06 -0700 (PDT) Received: from gamow.scripps.edu (gamow [137.131.252.67]) by relay1.scripps.edu (8.11.7/TSRI-4.2rAV) with ESMTP id h42FL7S00551; Fri, 2 May 2003 08:21:08 -0700 (PDT) Received: from quine.scripps.edu (dhcp-252-210 [137.131.252.210]) by gamow.scripps.edu (8.9.2/TSRI-3.0.1) with SMTP id IAA149553; Fri, 2 May 2003 08:21:07 -0700 (PDT) Received: by quine.scripps.edu (sSMTP sendmail emulation); Fri, 2 May 2003 08:21:22 -0700 Date: Fri, 2 May 2003 08:21:22 -0700 From: "David A. Case" To: Gitanjali Yadav Cc: chemistry@ccl.net Subject: Re: CCL:AMBER7/Cyclic Peptide Message-ID: <20030502152122.GB3772@scripps.edu> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.4i On Fri, May 02, 2003, Gitanjali Yadav wrote: > How can one make required input files for simulation of a > cyclic peptide in AMBER7. What I have is a starting coordinate > for this peptide in PDB format. See the instructions for LEaP, Chapter 5 of the Users' Manual. Basically, after loading the force field you want, you use the "loadPdb" command to read in the coordinates and sequence from the PDB file. There are detailed tutorials available at the Amber web site, http://www.amber.ucsf.edu/amber/ The best place to ask Amber-related questions is the Amber reflector: amber@heimdal.ucsf.edu (more info about this is on the web site, above). ..good luck...dac -- ================================================================== David A. Case | e-mail: case@scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ==================================================================