[gmx-users] question about pdb2gmx

Justin Lemkul jalemkul at vt.edu
Thu Jul 19 12:04:24 CEST 2012

On 7/19/12 5:00 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi everybody,
> I want to add protonation states to my protein with pdb2gmx.
> I now that there are the options:
> -lys -arg -asp -glu -his
> to do this.
> But was is about the cystein. How can I protonate this one?
> Is there also an option for it which I haven't seen?

The -ss flag controls cysteine protonation, in the sense that you can toggle 
between disulfide and free forms of cysteine.  Some force fields include an 
anionic form of cysteine as well.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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