[gmx-users] pdb2gmx and ignh

Tsjerk Wassenaar tsjerkw at gmail.com
Sat Aug 5 09:37:53 CEST 2006

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.



On 8/4/06, Frisco Rose <fmrose at ncsu.edu> 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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