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
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.
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Received on Tue Apr 12 2016 - 05:30:03 PDT
