[gmx-users] Adding Hydrogens by pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 31 13:18:47 CET 2011

James Starlight wrote:
> Dear Gromacs Users!
> I could not find how I can add missing hydrogens after their removing by 
> pdb2gmx -ignh.
> I have modified structure of my protein after editing by some soft and I 
> removed all hydrogens but now I want to add it back in accordance with 
> gromos ff topology
> How I can do it ?

They are removed and rebuilt entirely by pdb2gmx in accordance with the 
instructions found in the .hdb file.  If there are no hydrogens in the input, 
then -ignh is irrelevant.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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