Re: [AMBER] MC-MM-PBSA

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 21 May 2015 08:37:53 -0400

On Thu, May 21, 2015 at 1:46 AM, Ramin Ekhteiari <ramin_ekh.yahoo.com>
wrote:

> Hi dears,
> I have generated around 10,000 conformations for a complex
> (bound-receptor) using MC simulation and now I attempt to perform MM-PBSA
> calculation to estimate binding-free energy of these conformations. Each of
> the conformations is in .PDB format, so I would be grateful if you advise
> me on how to carry this process. The big question is that whether I should
> convert them to trajectory format or not. If so, how can I do it.
>

‚ÄčNo, you do not have to convert them to a trajectory. If you feed them all
to MMPBSA.py, then they will all be read, regardless of their format (so
long as cpptraj supports that file type):

MMPBSA.py -O -i mmpbsa.in -y *.pdb ... and so on

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 21 2015 - 06:00:03 PDT
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