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

Hagit G noolly at gmail.com
Wed May 2 12:55:28 CEST 2012

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?

Many thanks,
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