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
>
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Received on Tue Apr 12 2016 - 22:30:04 PDT
