[gmx-users] Trouble with pdb2gmx and cysteines

Steve stevesei at ymail.com
Wed Jan 15 20:32:12 CET 2014

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.


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