[gmx-users] Protein at given pH

Alexey Shvetsov alexxy at omrb.pnpi.spb.ru
Sat Dec 1 22:00:49 CET 2012

Justin Lemkul писал 07-11-2012 16:20:
> 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.

Actualy you can use data from h++ server with GROMACS. In order to do 
so you
1. amber files from H++ specificaly *.top and *.crd file
2. Install ambertools
3. Use ambpdb to create pdb file from *.top and *.crd something like 
ambpdb -p
*.top < *.crd > *.pdb
4. Get my script to renumber pdb and inset chain ids from
5. Process amber pdb file with it.
6. Feed it to gromacs and chose amber frocefield. Now it will use right
protonation states

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

Best Regards,
Alexey 'Alexxy' Shvetsov
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, 
Gatchina, Russia
Department of Molecular and Radiation Biophysics
Gentoo Team Ru
Gentoo Linux Dev
mailto:alexxyum at gmail.com
mailto:alexxy at gentoo.org
mailto:alexxy at omrb.pnpi.spb.ru

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