[gmx-users] binding_affinity

[shahid nayeem]

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