Hi,
No snapshot was attached. However, the output is exactly what it
should be (RMSD of each individual residue vs frame). Maybe you wanted
the 'perresavg' keyword?
-Dan
On Sat, May 2, 2015 at 12:37 PM, George Tzotzos <gtzotzos.me.com> wrote:
> I’m trying to work out the average rmsd over time of each residue in a protein receptor.
>
> The script I’m using is the following:
>
> parm 4fqt_OVT_solv.prmtop [MD]
> parm 4fqt_new.pdb [Xray]
> trajin prod_0-20ns.nc [MD]
> reference 4fqt_new.pdb parm 4fqt_new.pdb [4FQ]
>
> rmsd :10-125 reference perres perrescenter perresout PRMS.dat range 10-125 perresmask &!.H,N,CA,HA,C,O
> run
> xmgrace PRMS.dat
>
> I assume it is not correct as the output produced (see snapshot below) is not the expected one. In the x-axis instead of residue number, I get frame number.
>
> I’d appreciate any suggestions in correcting the above script.
>
> 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 Sat May 02 2015 - 16:00:02 PDT
