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
> >>
> >>
> >> _______________________________________________
> >> 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.
> > _______________________________________________
> > 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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
Received on Tue Apr 12 2016 - 22:30:03 PDT
