Sure. Use cpptraj and the 'strip' command. Something like:
parm myparm.parm7
trajin mytraj.nc
strip !(<mask specifying active site residues>)
trajout activesite.pdb
If residues 1, 2, 3, 4, 6, 7, and 11 are your active site residues,
the mask would be :1-4,6,7,11
-Dan
On Fri, Feb 24, 2017 at 2:36 PM, Thakur, Abhishek <axt651.miami.edu> wrote:
> Hi,
>
> I want to strip all the amino acids except form active site residues and make pdb file from trajectory. Can I do it?
>
> If yes how?
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Feb 24 2017 - 12:00:03 PST
