[gmx-users] atom H is missing in the first residue in a chain

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jan 15 08:47:28 CET 2009

Hi Justin/Zhong Zheng,

> Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens.
>  The problem is that, without -ignh, pdb2gmx expects all atoms (including H)
> to be present in the .pdb file.  If you are using a crystal structure, this
> requirement will not be satisfied.

It's actually almost opposite: -ignh ignores all hydrogens present,
thus stripping them from the .pdb file. The relevant ones are then
added back from the .hdb database. When you don't use -ignh pdb2gmx
expects all hydrogens in the .pdb file to correspond to atoms listed
for a residue in the .rtp file. If a hydrogen is not present it will
be rebuilt anyway, otherwise the position given will be used. The use
of -ignh is when you have hydrogen atoms listed that are not in the
force field description, like in an NMR file, processed for a united
atom force field. Crystal structures will usually process well without
-ignh, since no hydrogens are present to ignore in the first place :)



Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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