[gmx-users] Protein at given pH

[Steven Neumann]

On Wed, Nov 7, 2012 at 12:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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

Thank you for this!

Steven

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