Sorry for the delay in replying.
If all you want to do is select DCE within a certain radius of a
protein residue, your best bet is probably the 'mask' command in
cpptraj, e.g.
mask (:4<:7.0)&:DCE maskout selected.dat
This will select all residues named DCE within 7 Ang. of residue 4 and
write the results to selected.dat. Hope this helps,
-Dan
On Wed, Sep 9, 2015 at 1:30 AM, Neha Gandhi <n.gandhiau.gmail.com> wrote:
> Dear List,
>
> I have a protein adsorbed on the DCE (dichloro ethane) interface. I am
> trying to analyse contacts of DCE molecules with protein. I tried using
> contacts in cpptraj but it gives me total number of contacts. I am
> interested in figuring out the residue number of DCE making contact with a
> residue from protein. In summary I want to select DCE molecules within 7
> angstroms from the protein.
>
> Is there a way to do it in cpptraj? Your feedback is appreciated.
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Curtin Research Fellow,
> School of Biomedical Sciences,
> Curtin University,
> Perth GPO U1987
> Australia
> LinkedIn
> Research Gate
> _______________________________________________
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
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 Wed Sep 16 2015 - 08:00:03 PDT
