[AMBER] Visualyze avg structure in VMD

From: Valentina Romano <valentina.romano.unibas.ch>
Date: Tue, 5 Aug 2014 10:23:16 +0000

Dear amber users

I clustered a trajectory of protein-ligand complex with ptraj.
I would like visualize in VMD the average structure.
If I load it as PDB it looks really strange and I choose as format 'Amber coordinates" the molecule is not loaded.

Any suggestion?

Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |

Phone: +41 61 267 15 80

From: James Starlight [jmsstarlight.gmail.com]
Sent: Thursday, July 24, 2014 5:13 PM
To: AMBER Mailing List
Subject: [AMBER] Cpptraj clustering

Dear Amber users!

I'd like to use clustering method implemented in the Cpptraj to cluster big
set of conformers produced by Modeller as the result of the refirement of
some parts of my protein. For instance I has 1000 conformers with the
average <RMSD> ~ 0.5 which are structurally differs only in some flexible
(loops) regions => for simplicity in this case only in conformation of 1
longest loop. As the result I'd like to obtain projection of this
conformers onto plane of some subspaces where coordinated would correspond
to some structural criteriums (for instance percent of the occurence of
secondary structure elements detected in the refined (loop) region per
total number of conformers; and/or some geometrical criteriums like
distance between pair of residues, occurence of the salt-bridges etc. Could
such processing be performed by amber-tools taking into account that I have
amber-like trajectory consisted of my conformers ? On what parameters ( in
case of cluster utility for instance) should I pay a lot of attention?

Many thanks for suggestion,

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Received on Tue Aug 05 2014 - 03:30:02 PDT
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