[gmx-users] Protein at given pH

Justin Lemkul jalemkul at vt.edu
Wed Nov 7 13:20:12 CET 2012

On 11/7/12 7:10 AM, Steven Neumann wrote:
> On Wed, Nov 7, 2012 at 11:56 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> 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.
> Thank you Justin. So do not understand why this server produce pdb
> file which is redundant as you have to use -his -glu etc. flags
> anyway. According to pK - this server predicts pK for each residue and
> when my pH < pKa it is protonated, otherwise it is deprotonated,
> right? How about pH = pKa ?

If you're using the H++ server, it has no connection to Gromacs in any way. 
Your command line uses -ignh, so any hope of guessing the protonation state from 
the input is lost and thus you have to use interactive selection to counteract 
that effect or otherwise hope that all the atomic nomenclature is right so that 
pdb2gmx doesn't complain too much.

If pH = pKa, then your life is tougher.  In solution, 50% of the residues in the 
protein molecules will be protonated, 50% deprotonated.  You may have to model 
both protonation states if this is the case.



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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