[gmx-users] Protein at given pH

Justin Lemkul jalemkul at vt.edu
Wed Nov 7 12:56:33 CET 2012

On 11/7/12 4:19 AM, Steven Neumann wrote:
> Dear Gmx Users,
> I am trying to simulate protein-ligand interactions at specific pH=5.
> I processed my protein.pdb into the H++. As I see from th titration
> curve of the entire molecule it appears that at pH=5 the total charge
> should be equal to 2. When I process the obtained pdb from the server
> to pdb2gmx using -ignh I get the total charge of -3. Can anyone
> explain me this?

pdb2gmx chooses protonation states based on the assumption that you're working 
at neutral pH.  If you want some alternate protonation state for certain 
residues, you have to choose them yourself using the various options that 
pdb2gmx provides for this purpose.

> In terms of small molecules how can I get parameters at specific pH? I
> am using Charmm and parachem.org does not support pH changes. Can
> anyone advise?

pKa values for most common groups should make the protonation state at a given 
pH fairly straightforward, otherwise you need to calculate the pKa's in some way 
and adjust the molecule's protonation accordingly.



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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