[gmx-users] Adding Hydrogens by pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 31 13:27:13 CET 2011

James Starlight wrote:
> Its very unclear for me because after pdb2gmx -f 1.pdb -o conf.gro 
> -ignh  with gromos force field
> I've checked conf.gro by VMD and this structure didnt contains any 
> hydrogens ;o

I highly doubt that.  I've used one of the Gromos96 force fields for nearly all 
of my work and it has never failed in any Gromacs version.  Perhaps you're 
simply not taking into account the fact that Gromos96 parameter sets are united 
atom, meaning that aliphatic hydrogens are not represented explicitly.



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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