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.
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--
-------------------------
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 Tue Apr 12 2016 - 13:00:03 PDT
