Re: topology file generation

From: Andreas Svrcek-Seiler <svrci_at_tbi.univie.ac.at>
Date: Mon 6 May 2002 14:11:54 +0200 (CEST)

Hi,
> Hello,
> I would like to automate generation of topology file for a large
> number of PDBs.
...
Provided your pdbs are 'clean', the easiest way to do this
that comes to my mind is using NAB:

the following NAB 'program' reads in a pdb file
and writes out a prmtop file ( named 'prmtop'):


molecule m;
m=getpdb(argv[2]);
leap(m,"","");


so, if you have your pdb files in one directory,
you might do something like (in tcsh and with the above 'program' compiled
to 'makeprmtop' ):

foreach i (*.pdb)
makeprmtop ${i}
mv prmtop ${i}.prmtop
end

hope it helps,
regards
Andreas

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Received on Mon May 06 2002 - 05:11:54 PDT