[gmx-users] Trouble with pdb2gmx and cysteines

Mark Abraham mark.j.abraham at gmail.com
Wed Jan 15 23:42:13 CET 2014


You're saying you've got two cysteines close enough that a bond might be
reasonable and the output from pdb2gmx had nothing relevant to say?


On Wed, Jan 15, 2014 at 8:31 PM, Steve <stevesei at ymail.com> wrote:

> Hello
> I am trying to make CYS in my topology file (and NOT CYSH or dissulfide
> bond). If my pdb file calls for Cys, I get CYSH .rtp type.
> I Then attempted to test the -ss command using pdb2gmx and this command is
> completely ignored. I don't get an error or any output suggesting its
> usage.
> I am using version 4.5.4
> How can I distinguish between CYS, CYSH???
> Any help would be greatly appreciated. I did look in the mailing list, but
> I
> could not find anything that helped.
> Thanks
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