gutierrezangel wrote:
On Sunday 08 April 2012 12:00:06 [email protected] wrote:
Is there a tool with which you can charge a protein after a certain
pH-value?
What about H++?
http://biophysics.cs.vt.edu/
H++ is a good tool for estimating pKa values. It is from these results that one
can make a decision about the protonation state to specify with pdb2gmx. It is
not clear to me what exactly the original question is, but if it is a matter of
assigning protonation states for the predominant form of titratable residues in
a protein at a given pH value, one can set these states using pdb2gmx.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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