From chemistry-request@server.ccl.net Mon Jan 15 12:39:22 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 f0FHdLd14875 for ; Mon, 15 Jan 2001 12:39:21 -0500 Received: from localhost (rvenable@localhost) by gandalf.cber.nih.gov (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id MAA42717; Mon, 15 Jan 2001 12:33:49 -0500 (EST) Date: Mon, 15 Jan 2001 12:33:49 -0500 From: Rick Venable To: "Dr. Richard Wood" cc: chemistry@ccl.net Subject: Re: CCL:babel development? In-Reply-To: <3A63130D.DD7335CB@cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > David van der Spoel wrote: > > Is anybody still actively developing/maintaining babel? The latest version > > (1.6) seems to be from 1996. > > ________________________________________________________________________ > > Dr. David van der Spoel Biomedical center, Dept. of Biochemistry > > s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden > > e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel > > phone: 46 18 471 4205 fax: 46 18 511 755 > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ On Mon, 15 Jan 2001, Dr. Richard Wood wrote: > This is an interesting question, because Babel is SUPPOSED to be > able to read CHARMM files as input, yet it doesn't. And since there > is no program other than Quanta that will allow one to easily view > CHARMM crd files, it would be nice to be able to convert them to > some other format, > -- > Richard L. Wood, Ph. D. > Physical/Computational Chemist > Post-doctoral Associate > Cornell University, Ithaca, NY 14853 Actually, I believe that both Rasmol and VMD can read and display CHARMM .crd files, and write them back out in PDB format. For Rasmol, the process requires using the command line, and can't be automated easily; something like load charmm file.crd save pdb file.pdb should handle the file format conversion. Note, however, that there are a few naming conflicts for amino acids between CHARMM and PDB, for both residue names (HIS) and heavy atom names (ILE, C-terminal O). For molecules besides the standard 20 amino acids, e.g. cofactors and AA analogs, there is considerably more divergence in naming. My experiences with automated coordinate file conversion have, in general, not been very good, esp. with Babel. Conversions from Cambridge FDAT to PDB are particularly bad; all the numeric atom labels are discarded, and all carbons become simply 'C' instead of 'C1', 'C2', etc. I realize that these are arbitrary numeric labels assigned by the crystallographer and don't necessarily correspond to IUPAC numbering, but they would be useful if retained. (I developed my own procedure, using Cambridge 'quest' prog directly, and a little file editing.) =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= 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 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=