Then would not you expect these two separate scripts for ptraj and cpptraj
should produce the same results in perresavg.dat and RMSF output files
cpptraj_rmsf.in
parm Filename.prmtop
reference Filename.inpcrd
trajin Filename.mdcrd
rms reference :1-128 perres perresout rms_vs_time.dat perresavg
perresavg.dat
ptraj_rmsf.in
trajin Filename.mdcrd 1 10000000 1
reference Filename.inpcrd
rms reference :1-128
atomicfluct out RMSF :1-128 byres
On Fri, Jun 27, 2014 at 7:07 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
regards
Bharat Lakhani
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Received on Mon Jun 22 2015 - 10:00:03 PDT
