Ho THANKS MANY THANKS I'm sorry, I'm new to Gromacs, and finally got it. Thank you very much.
Hagit. 2012/5/2 Mark Abraham <mark.abra...@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 > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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