Dear Valentina,
For visualization, you'll want to look at a representative structure, not
an average structure (as coordinates are averaged, which leads to a
'strange' view). I *think* the required cpptraj cluster option to write a
representative structure depends on the AmberTools version you use, so
please check the manual.
(Always load PDB formatted files as PDB in VMD, not Amber coordinates.)
--Marc
On 5 August 2014 11:23, Valentina Romano <valentina.romano.unibas.ch> wrote:
> 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?
>
> Best,
> Valentina
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> 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 А 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,
>
> James
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Received on Tue Aug 05 2014 - 04:00:02 PDT
