Subject: Re: CCL:babel development?

From: Rick Venable <[email-masked]>
Date: Mon, 15 Jan 2001 12:33:49 -0500

> 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: [email-masked]    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.)

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Rick Venable
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905
[email-masked]
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