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

Mark Abraham Mark.Abraham at anu.edu.au
Wed May 2 15:11:08 CEST 2012

On 2/05/2012 8:55 PM, 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?

Yes, and the clue to how to combine the chains to give the mechanism a 
chance of working is on the page I linked last time: 

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