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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