ptraj instructions are in the ambertools manual (a separate download). You
should look up the
ambermask to see how to parse this example ptraj input file. In this case it
will print out the distance
between the carbon alpha atoms of the 2nd and 8th residues.
--Dan
On Sun, Feb 20, 2011 at 6:11 PM, Cheng-I Lee <biocil.ccu.edu.tw> wrote:
> Dear Amber users,
>
> I have followed the AMBER tutorial A7 for REMD simulation.
> In analysis of the REMD results, reolica trajectories can be extracted by a
> script named create_replica_trajs.x
> In this script, what kind of distance information is obtained?
>
> ptraj ala10.prmtop << EOF
> trajin remd.mdcrd.$ext
> trajout remd.reptraj.$ext nobox
>
> distance d1 out dist.rep.$ext :2.CA :8.CA
>
> Also, the manual of AMBER 11 does not include the section of ptraj. I
> assumed that ptraj in AMBER 11 works as same as in AMBER 9.
>
> Thanks!
> Sophia
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
--
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 20 2011 - 06:00:05 PST
