[gmx-users] binding_affinity

[Justin A. Lemkul]

shahid nayeem wrote:
> Hi Justin
> I went through your tutorial of umbrella sampling. Please clarify that
> while generating configuration one requires index.ndx of certain
> residue. These residue are from the restrained chain or from the chain
> on which pulling force is to be applied in order to separate the
> chain. why two groups are created. Does index.ndx should contain all
> residue from the chain which has to move or few are sufficient.

Do what is appropriate for your system.  The reasons for the restraints I used 
are described in my paper that I link from the tutorial.  I certainly hope 
you've read it to understand the methodology.  Thus you do not necessarily have 
to apply the exact methodology to get a sensible result.

You need two groups - a reference group and a group to which the pulling force 
is applied.  Maybe your reference group (whatever it is) needs to be restrained 
to avoid structural deformation, maybe it doesn't.  Whether or not an index file 
is necessary also depends on how you set up the reference and pulled groups.  If 
they are default groups, then you don't need an index file, but if they are some 
subset of existing groups, then yes, you need a custom index file, just like any 
other Gromacs operation.

-Justin

> Shahid Nayeem
> 
> On Thu, Apr 14, 2011 at 6:34 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> shahid nayeem wrote:
>>> Dear All
>>> I have some protein complex pdb after docking two monomers. The
>>> scoring of these docked structure are not true representative of
>>> binding affinity. I want calculate the binding affinity affinity of
>>> these docked pdb. Can anyone suggest me, how should I proceed.
>>> Shahid Nayeem
>> Calculating a PMF is a common approach.
>>
>> http://www.gromacs.org/Documentation/How-tos/Potential_of_Mean_Force
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> 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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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================