[gmx-users] How to remove H atom from residue in gro file?

Justin A. Lemkul jalemkul at vt.edu
Wed May 2 15:09:39 CEST 2012

On 5/2/12 6:55 AM, Hagit G wrote:
> Hi gmx users,
> Well, I saw this question but the answer was not understood.
> I'm trying to work with the file 1PPB.pdb. There are 2 chains connected with a
> disulfide bond. Gromacs automatically adds H atoms.
> Although the disulfide bond is there, Gromacs ignore it because *each cystein is
> on a different chain*. So it adds H and therefor the disulfide bond is ruined
> during energy minimization.
> Is there any way to recreate such a disulfide bond (Please don't tell me again
> about "-ss" it works only on one chain. Moreover, the bond is existed on the pdf
> file.) or never ruined it at the first place?

Well you may need to use -ss, but since you don't want to hear about it, I won't 
say anything more...

What you need to do is create a [moleculetype] that consists of both chains. 
The pdb2gmx option -chainsep will allow you to create a properly merged molecule 
that can form the intermolecular disulfide because the two molecules will be 
considered as one [moleculetype], as Gromacs requires.



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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