On 7/19/12 5:00 AM, [email protected] 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
--
========================================
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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