Dear Dan;
Thank you so much for pointing it out. And yes we are looking at
filtering.Lets see what comes up in binding free.
Thank you again very much.
On Mon, Jun 23, 2014 at 3:58 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Mon Jun 23 2014 - 07:30:03 PDT
