While generating rmsd graph using xmgrace it is giving in angstrom units. I
wanted to get in nanometers from the graph.
On Wed, Apr 13, 2016 at 10:42 AM, Andy Watkins <andy.watkins2.gmail.com>
wrote:
> An angstrom is a tenth of a nanometer, so you can divide by ten.
>
> On Tue, Apr 12, 2016 at 10:06 PM, Sreemol G <sreemolinfo.gmail.com> wrote:
>
> > Once again I have gone through the tutorial and it is fine now. One more
> > thing i want to know, Is it possible to get RMSD values in nanometers
> > instead of angstrom unit???
> >
> >
> > On Wed, Apr 13, 2016 at 1:20 AM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> >
> > > On Tue, Apr 12, 2016 at 6:13 AM, Sreemol G <sreemolinfo.gmail.com>
> > wrote:
> > > > Thank you.. But masking :1-177.C,CA,N will take residues only from
> > > protein
> > > > molecule. But i want to calculate backbone RMSD for protein-RNA
> > complex.
> > > I
> > > > have gone through the manual and it was little confusing. could you
> > > please
> > > > tell me the exact command to generate single RMSD graph for
> protein-RNA
> > > > complex??
> > > > these are the atoms i want to mask in RNA.
> > > > :178-199.P,O3',C3',C2',O2',HO2',C1',O5',O4',C5',C4'
> > > > and for protein :1-177.C,CA,N
> > >
> > > Try the mask :1-177.C,CA,N|:178-199.P
> > > ,O3',C3',C2',O2',HO2',C1',O5',O4',C5',C4'.
> > > Did you try going through the tutorial as Anselm suggested? If not I
> > > highly recommend it.
> > >
> > > -Dan
> > >
> > > >
> > > > On Tue, Apr 12, 2016 at 5:15 PM, David A Case <
> david.case.rutgers.edu>
> > > > wrote:
> > > >
> > > >> On Tue, Apr 12, 2016, Sreemol G wrote:
> > > >>
> > > >> > Can anyone explain what this 2.0 :2 denotes in this command
> > > >> > "rms reference mass out 02_03.rms time 2.0 :2"
> > > >>
> > > >> The "2.0" is an argument to the "time" keyword, and specifies the
> time
> > > >> between
> > > >> snapshots in the trajectory file. This can be in whatever units you
> > > >> choose.
> > > >>
> > > >> The ":2" is a mask, specifying that you want to do an RMS fit on the
> > > atoms
> > > >> in
> > > >> residue 2 (only). This is unlikely to be what you want. As Dan
> > pointed
> > > >> out earlier, you probably want a mask that looks something like
> > > >> :1-177.C,CA,N.
> > > >>
> > > >> ...dac
> > > >>
> > > >>
> > > >> _______________________________________________
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> > > >>
> > > >
> > > >
> > > >
> > > > --
> > > > With kind regards,
> > > > G. Sreemol
> > > > M.Tech (Computational Biology)
> > > > Anna university
> > > > Chennai.
> > > > _______________________________________________
> > > > 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)
> > >
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> > >
> >
> >
> >
> > --
> > With kind regards,
> > G. Sreemol
> > M.Tech (Computational Biology)
> > Anna university
> > Chennai.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With kind regards,
G. Sreemol
M.Tech (Computational Biology)
Anna university
Chennai.
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Received on Tue Apr 12 2016 - 22:30:06 PDT
