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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 01 2016 - 03:00:03 PST
