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, Hagit.
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