Re: CCL:babel development?

[Rick Venable <rvenable "-at-" gandalf.cber.nih.gov>]

 > 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 "-at-" xray.bmc.uu.se    www: http://zorn.bmc.uu.se/~spoel
 > > phone:  46 18 471 4205          fax: 46 18 511 755
 > >
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 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
 Rick_Venable "-at-" nih.gov
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