[gmx-users] Protein at given pH

Steven Neumann s.neumann08 at gmail.com
Wed Nov 7 13:10:51 CET 2012

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 ?


>> 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
> --
> ========================================
> 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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