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

Hagit G noolly at gmail.com
Thu May 3 12:01:04 CEST 2012


I'm sorry, I'm new to Gromacs, and finally got it. Thank you very much.


2012/5/2 Mark Abraham <Mark.Abraham at anu.edu.au>

>  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:
> http://www.gromacs.org/Documentation/How-tos/Making_Disulfide_Bonds
> Mark
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