Ok.
Thank you sir
I wil try this.
On Wed, Dec 7, 2016 at 1:39 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> This is almost right, but what you want to do is RMS-fit the DNA
> _before_ you cluster, then cluster on your ligand using 'nofit'. So
> something like:
>
> parm myparm.parm7
> trajin mytraj.nc
> rms first <DNA backbone mask>
> cluster <ligand mask> nofit ...
>
> Hope this helps,
>
> -Dan
>
> On Thu, Dec 1, 2016 at 5:43 AM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
> > Sir
> >
> > Thank you very much.
> >
> > This is a sample given in amber tutorial
> >
> > trajin traj.1.gz
> > trajin traj.2.gz
> > cluster out testcluster representative pdb average pdb averagelinkage
> > clusters 5 rms .CA
> >
> > Is the mask part you mentioned "rms .CA" ?
> >
> > Are you familiar with mmtsb (i always use mmtsb as learned from amber
> > tutorial) ? And do you know any keyword related to this?
> >
> > thanking you
> >
> > On Thu, Dec 1, 2016 at 3:56 PM, Achim Sandmann <
> > Achim.Sandmann.chemie.stud.uni-erlangen.de> wrote:
> >
> >> Hello Mary Varughese,
> >>
> >>
> >> So far as I understood, you want to take the ligand position with
> >> respect to the DNA (as well as the ligand conformation itself) into
> >> consideration.
> >>
> >> I think the easiest way to do this is to do a RMSD calculation with the
> >> DNA backbone mask first. This will align the structures. As a second
> >> step (within the same praj/cpptraj call) you can use the cluster command
> >> with the mask of the ligand and the 'nofit' flag.
> >>
> >>
> >> with kind regards,
> >>
> >> Achim Sandmann
> >>
> >>
> >> Am 01.12.2016 um 08:26 schrieb Mary Varughese:
> >> > Sir
> >> >
> >> > I have a DNA ligand system. After aligning all the structures with
> >> respect
> >> > to DNA backbone i want to cluster on the basis of ligand
> conformation. Is
> >> > there any way to specify that aspect in mmtsb or ptraj cluster.
> >> >
> >> > Thanking you
> >> >
> >> >
> >> > mary varughese
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >> _______________________________________________
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> >>
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>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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Received on Tue Dec 06 2016 - 21:00:02 PST
