[gmx-users] binding_affinity

[Justin A. Lemkul]

shahid nayeem wrote:
> Hi Justin
> Thanks a lot. What is the purpose of adding 100mM NaCl. Is it
> mimicking physiological condition.

More of a hybrid of physiological and in vitro conditions.  Please see the 
referenced paper for more details.

-Justin

> Shahid Nayeem
> 
> 
> On Tue, Apr 19, 2011 at 5:47 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> 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
>>
>> ========================================
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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

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