All programs in Amber use the AKMA units system, so distances are
always in Angstroms. If you want nm, you'll have to convert as
suggested by Andy. For example:
rms R1 first :1-177
run
R1_nm = R1 / 10.0
writedata R1.out R1_nm
-Dan
On Tue, Apr 12, 2016 at 11:16 PM, Sreemol G <sreemolinfo.gmail.com> wrote:
> 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
>> > > >>
>> > > >>
>> > > >> _______________________________________________
>> > > >> 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
>> >
>> _______________________________________________
>> 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)
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Received on Wed Apr 13 2016 - 05:30:03 PDT
