[gmx-users] Re: Protein charge

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 8 18:02:47 CEST 2012

gutierrezangel wrote:
> On Sunday 08 April 2012 12:00:06 gmx-users-request at gromacs.org 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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