I don't think there's anything wrong with your script - from the Amber
15 manual:
...
perresout <perresfile> Write per-residue RMSD to <perresfile>.
perresavg <avgfile> Write average per-residue RMSDs to <avgfile>.
...
So it sounds like what you want might be 'perresavg'.
-Dan
On Tue, Aug 18, 2015 at 8:47 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Following the AmberTools15 manual (p. 552), I’m using the following input scrip to do a per-residue RMSD calculation:
>
> parm complex_solv.prmtop
> trajin prod_0-100ns.nc 1 10000 10
> reference complex_solv.inpcrd [struct0]
> rmsd A :11-125 ref [struct0] perres perresout PRMS.dat range 11-125 perrescenter perresmask &!.H,N,CA,HA,C,O
> run
> xmgrace PRMS.dat
>
> Obviously there is something wrong with the script because instead of producing an x-axis with residue numbers, the x-axis represents frame number.
>
> I’d appreciate any suggestions on how to improve the script to generate per-residue RMSD averaged over the trajectory time.
>
> Regards
>
> George
> _______________________________________________
> 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 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 18 2015 - 08:00:07 PDT
