Re: [AMBER] clustering doubt

From: Achim Sandmann <>
Date: Thu, 1 Dec 2016 11:26:24 +0100

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

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 mailing list
Received on Thu Dec 01 2016 - 02:30:02 PST
Custom Search