Hi,
Sounds like you might want to use the 'perres' keyword for the 'rmsd'
command. This will calculate the no-fit RMSD for residues specified by
the 'range' keyword within the reference frame of the rms-fit defined
by '<mask>'. See the manual for more details.
Hope this helps,
-Dan
On Wed, Jan 13, 2016 at 12:02 AM, Vertika Gautam
<vartikapisces.gmail.com> wrote:
> Hi
>
> I have calculated the RMSD of all residues of the my protein protein
> complex.
> using the input
>
> trajin ../05-production1ns.mdcrd
>
> trajin ../05-production2ns.mdcrd
>
> trajin ../05-production3ns.mdcrd
>
> trajin ../05-production4ns.mdcrd
>
> trajin ../05-production5ns.mdcrd
>
> trajin ../05-production6ns.mdcrd
>
> trajin ../05-production7ns.mdcrd
>
> trajin ../05-production8ns.mdcrd
>
> trajin ../05-production9ns.mdcrd
>
> trajin ../05-production10ns.mdcrd
>
> reference ../uv7.crd
>
> rms reference out rmsd_allcpx.plot :1-498
>
> rms reference out rmsd_allrec.plot :1-344
>
> rms reference out rmsd_allLigand.plot :345-498
>
> rms reference out rmsd_bbcpx.plot :1-498.CA,C,N,O
>
> rms reference out rmsd_bbrec.plot :1-344.CA,C,N,O
>
> rms reference out rmsd_bbLigand.plot :345-498.CA,C,N,O
>
>
>
> now I want to calculate for selected residues from the receptor, lets say
> residues 181-257. Could you please tell me how to change the rmsd input?
>
>
>
> Thanks in advance
> --
> Vertika Gautam
>
>
>
>
>
> *e-mail address: vartikapisces.gmail.com
> <vartikapisces.gmail.com>
> vartikapisces.hotmail.com <vartikapisces.hotmail.com>
> 01112294191*
> _______________________________________________
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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 Wed Jan 13 2016 - 09:00:08 PST
