Thanks Daniel!!
It works.
On Jan 14, 2016 12:51 AM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> 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*
> > _______________________________________________
> > 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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>
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Received on Sat Jan 16 2016 - 00:00:03 PST
