Mark Abraham wrote:
Jones de Andrade wrote:
Hi Tsjerk.
Thanks for the prompt answer.
Good idea, I can take the atom names from a .gro file, nad, probably
some strange algorithm can also get the number of atoms per molecule
and number of molecules from there, am I right? That would help a lot.
Simplest is to write a parser for a gmxdump of a .tpr file. This is what
Perl was made for. If you're constrained to use Fortran for your
analysis program, then developing an intermediate file format for it to
parse might be worthwhile.
But: I'll still be unable to get atomic masses and point charges. No
to mention the box shape. :( And I'll need a way to read these
parameters too, unless I begin to write all them in a really awfull
and strange index file.
From what I can understand on the "file logistics" of gromacs, these
information are only stored in the whole ".top .itp .atp .rtp
structure of files" or, in a condensed form, in the ".tpr" file. Is
that right?
Yeah. Writing something to do the lookups in the .*tp files which grompp
does to form the .tpr is asking for trouble. Do the lookup in the .tpr
file. The .edr file has box dimensions, of course.
All this makes it sound like you should be dropping Fortran and writing
in C or Perl!
the box is in the xtc file, if you need the atom names a corresponding
pdb or gro file should do the trick. don't try to read tpr files or
gmxdumps of it, that's a complete waste of time. you can e.g. use
editconf to dump a pdb file with charges in the b-factor fields.
And indeed, using fortran will make your life quite miserable for these
kind of things.
--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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