[gmx-users] Using .pdb only

Justin A. Lemkul jalemkul at vt.edu
Mon Sep 1 14:40:08 CEST 2008

vivek sharma wrote:
> Hi There,
> I am usinng gromacs for running MDS of one protein, Can I use the pdb 
> file only without generating the .gro file i.e. without using pdb2gmx ?

Theoretically, yes.  Gromacs can read a number of file formats at any stage 
(.pdb, .gro, etc).

> If no, then how can I avoid addition of hydrogen during pdb2gmx ?

Then you will probably have a broken (and useless) topology.  Addition of 
hydrogens is dependent upon the force field you want to use.  All atomistic 
force fields distributed with Gromacs require at least the inclusion of polar 


> With Thanks,
> Vivek
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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