[gmx-users] question about pdb2gmx

[Justin Lemkul]

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

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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