If you just want the backbone RMSD you will need to modify your atom
masks to only include backbone atoms; ':1-199' selects all atoms from
residues 1 to 199. For your protein residues, you could do something
like ':1-177.C,CA,N' etc. See the Amber 15 manual section 29.1.6 for
more information and examples of the Amber atom mask selection syntax.
-Dan
On Fri, Apr 8, 2016 at 5:04 AM, Sreemol G <sreemolinfo.gmail.com> wrote:
> I need to calculate backbone RMSD for Protein-RNA complex. the command
> given below is the one i used to calculate backbone RMSD, I would like to
> know whether it is sufficient to cover all the information about both
> protein and RNA backbone. I have 199 residues in my complex. Among them 177
> are amino acids and 22 are RNA.
>
> trajin md1.mdcrd
> trajin md2.mdcrd
> rms first out backbone.rms :1-199
>
>
> On Fri, Apr 8, 2016 at 3:00 PM, Dr. Anselm Horn <anselm.horn.fau.de> wrote:
>
>> Dear Sreemol,
>>
>> > I have done simulation for protein-RNA complex for 10 ns, I want to
>> > calculate the backbone RMSD for the complex. How to calculate the
>> backbone
>> > RMSD for protein-RNA complex.
>>
>> backbone RMSD calculations are a very basic analysis technique. For such
>> analyses, many people have created excellent tutorials available from
>> the amber webpage ambermd.org. A first example of the RMSD analysis is
>> given in the very first tutorial:
>>
>> http://ambermd.org/tutorials/basic/tutorial0/
>>
>> The second tutorial deals with DNA, so you might also want to have a
>> look at that.
>>
>> Additionally, the documentation of the Amber suite contains a detailed
>> description of all programs and input parameters (cf
>> http://ambermd.org/doc12/).
>>
>> All the best,
>>
>> Anselm
>>
>> Dr.rer.nat.
>> Bioinformatik
>> Friedrich-Alexander-Universität Erlangen-Nürnberg
>> Germany
>>
>>
>> _______________________________________________
>> 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 Fri Apr 08 2016 - 09:30:03 PDT
