[gmx-users] binding_affinity

shahid nayeem msnayeem at gmail.com
Tue Apr 19 14:13:32 CEST 2011

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.
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
> 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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