The results will be qualitatively similar but not the same as they are
fundamentally different calculations. The atomic fluctuations are
essentially the variance in coordinates of each atom over the course of a
simulation, and the byres keyword converts that to the average over the
residue weighted by the mass of each atom. In contrast, the average per
residue RMSD measures the average deviation in all coordinates of that
residue after the global best-fit.
-Dan
On Mon, Jun 22, 2015 at 10:59 AM, bharat lakhani <lakhbharat.gmail.com>
wrote:
> 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
> _______________________________________________
> 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
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 23 2015 - 08:00:05 PDT
