On Fri, Nov 28, 2014 at 12:26 AM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> Dear Amberists;
>
> I have a protease with two monomer. I wish to calculate interaction energy
> between two monomer subunits during simulation time. I will appreciate if
> someone helps via the script by which I can able to calculate the
> monomer-monomer interaction energy.
>
> Suppose :1-99 (monomer 1) and 100-198 (monomer 2).
>
> Thank you in advance for your help and time.
>
You can use MM/PBSA or MM/GBSA analyses to get this interaction energy,
potentially. ante-MMPBSA.py can help you generate the prmtop files you'll
need for the analyses and MMPBSA.py can be used to compute the interaction
energy. Details can be found in the manual.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Nov 28 2014 - 16:30:02 PST
