[gmx-users] Hydrogen atoms type

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 4 13:55:11 CEST 2011

Amir Abbasi wrote:
> Hi Dear Users!
> I'm Using MMB to produce initial structures for my simulations.
> This program creating a .pdb file in output.
> The output file containing Hydrogen atoms that are not recognized by 
> gromos53a5.
> I want to edit my pdb file but I can't find anything about "hydrogen 
> types in gromos"!
> any suggestion?

The Gromos force fields are united-atom, so most H atoms are not used.  Aromatic 
hydrogens are type HC and polar hydrogens are type H.

If you're trying to run your structure through pdb2gmx and it's complaining, use 
-ignh and only necessary hydrogens will be built back on.



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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