Hi,
Just to expand on what Jason said, you probably want something like this:
parm myparm.parm7
reference myref.rst7
trajin target.nc
rms <mask> reference perres perresout rms_vs_time.dat perresavg
perresavg.dat
rms_vs_time will contain per-residue RMSD for each residue, perresavg.dat
will contain the average per-residue rmsd over all frames for each residue.
See the manual for more details on these and other keywords.
Hope this helps,
-Dan
On Fri, Jun 27, 2014 at 4:50 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Fri, Jun 27, 2014 at 5:46 PM, Chinthaka Ratnaweera <cnr88.msstate.edu>
> wrote:
>
> > This is not I meant.
> > Lets say, I have two pdb structures of the same protein, which generated
> > through average md trajectories after different interactions. These two
> > structures are slightly different. I want to find out the rmsd between
> > them. I know VMD can do that. But I want to know whether it is possible
> in
> > ptraj or cpptraj?
> >
>
> Yes. cpptraj can do it. If you type "help rmsd" in the cpptraj command
> prompt, you will see a "perres" keyword that should do what you want it to
> do.
>
> *$* cpptraj
>
>
> CPPTRAJ: Trajectory Analysis. V15.01b
>
> ___ ___ ___ ___
>
> | \/ | \/ | \/ |
>
> _|_/\_|_/\_|_/\_|_
>
> > help rmsd
>
> [<name>] <mask> [<refmask>] [out filename] [nofit | norotate] [mass]
>
> [ first | reference | ref <name> | refindex <#> |
>
> reftraj <filename> [parm <parmname> | parmindex <#>] ]
>
> [perres perresout <filename> [perresavg <avgfile>]
>
> [range <resRange>] [refrange <refRange>]
>
> [perresmask <additional mask>] [perrescenter] [perresinvert]
>
> Calculate coordinate root-mean-squared deviation of atoms in <mask>
> >
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> 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 201
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 Fri Jun 27 2014 - 16:30:02 PDT
