Hi,
What you are talking about doing isn't really clustering per se; it's more
like filtering/binning.
On Mon, Jun 23, 2014 at 7:51 AM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
>
> trajin *md1.mdcrd*
> rms R1 first :1-198 .CA
> outtraj frames_rms1_md1.mdcrd maxmin R1 min 0.0 max 1.0
>
This will work in older versions of CPPTRAJ; in the latest version (14)
this functionality has been separated from outtraj and is now the 'filter'
action:
trajin md1.mdcrd
rms R1 first :1-198.CA
filter R1 min 0.0 max 1.0
trajout frames_rms1_md1.mdcrd
Note there is no space between ':1-198' and '.CA'; masks should have no
spaces in them unless they are enclosed in quotes.
>
> Please suggest if this script looks good for this process. And any way to
> calculated binding free energy on these extracted frames.
>
You could probably use an MMPBSA-type approach to do this, assuming you
still have enough frames to get good statistics.
Hope this helps,
-Dan
>
> Help and suggestion regarding this will be highly appreciated.
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
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>
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Jun 23 2014 - 07:30:02 PDT
