Hi Frisco,
Are you by chance using a _united_ atom force field (GROMOS?). And are
you wondering where all you're non-polar hydrogens are? Please read
the manual (better) and read the papers about the force field you're
using. -ignh strips all hydrogens, which is handy if there are
hydrogens present which shouldn't be there according to the
description in the force field. In that case, all hydrogens which
should be there, according to the force field, are added bakc
according to a set of geometrical rules.
I hope this answers your question.
Cheers,
Tsjerk
On 8/4/06, Frisco Rose [EMAIL PROTECTED] wrote:
Hello all,
I am confused about what the -ignh option of pdb2gmx actually does. I
have read the mailing list, the manual and many tutorials and short of
browsing the source cannot find a definite answer.
The man page claims that pdb2gmx will add hydrogens, however after using
the ignh option to ignore inappropriately named hydrogens in the input
pdb (1xq8.pdb) there are many missing hydrogens (nearly a thousand - as
far as I can tell) in the output files.
Running any calculation with that many missing hydrogens seems very
non-physical. It seems that pdb2gmx doesn't like the naming conventions
or number of hydrogens in the pdb file.
Can someone please explain what -ignh actually does and what the proper
method of converting a pdb file from RCSB for use with GROMACS should
be? I have tried building the protein from scratch with pymol but
pdb2gmx doesn't like pymol generated pdb files either.
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--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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