Hi,
On Mon, Feb 5, 2018 at 11:28 AM, MOHD HOMAIDUR RAHMAN
<rahmanhpu.gmail.com> wrote:
>
> Now I want to extract the lowest energy snapshot pdb from trajectories to
> represent possible structure free energy landscape.
You can search for and extract the lowest potential energy structure
via energy post processing with sander (imin=5) and cpptraj, but that
may not be a good representative of the free energy minimum since that
will also depend on system entropy. To that end you are probably
better off using something like the representative structure from the
most populated cluster obtained from cluster analysis, but whether
that will actually be representative of your free energy minimum will
largely depend on the quality of your sampling. For more on sampling
in MD simulations I recommend checking out the following article:
https://pubs.acs.org/doi/abs/10.1021/ct400862k
Hope this helps,
-Dan
>
> I am looking for any possible modules or option is available in AmberTools
> to do this job.
>
> Thank you in advance.
> Regards
> Rahman
>
> '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
> *M*d* H*omaidur* R**ahman *( Research Scholar )
> Lab No. 510, Computational Biophysics Lab.
> Department of Biotechnology
> Indian Institute of Technology-Madras
> Chennai-600 036, India
> *Mobile No = +91- 7845991785*
> '''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Feb 09 2018 - 04:30:02 PST
