[gmx-users] Protein at given pH

[Alexey Shvetsov]

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
need
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
http://biod.pnpi.spb.ru/~alexxy/h++/pdbfix.pl
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