[gmx-users] Umbrella sampling-protein-ligand complex

[Archana Sonawani]

Dear Justin,

So do I have to carry out umbrella sampling simulations separately for the
three complexes or put the three ligands together with the protein and pull
the ligands one by one to calculate the binding energy. I am confused.

Thanks in advance.

Regards,

Archana

On Fri, Sep 28, 2012 at 8:00 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 9/28/12 9:27 AM, Archana Sonawani wrote:
>
>> Hi,
>>
>> I have performed simulations for 3 different ligands complexed with the
>> same protein. I want to compare the binding energies of these different
>> three complexes. Will umbrella sampling be useful in this case?
>>
>>
> Several methods could be used, and umbrella sampling is certainly one of
> them.
>
> -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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-- 
Archana Sonawani-Jagtap
Junior Research Fellow,
Biomedical Informatics Centre,
NIRRH (ICMR), Parel
Mumbai, India.
9960791339