Hi,
On Tue, Aug 5, 2014 at 4:23 AM, Valentina Romano
<valentina.romano.unibas.ch> wrote:
> 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.
Remember that an average structure does not necessarily reflect
reality; for example, if you have a methyl group rotating, the average
position of the hydrogens will be somewhere near their collective
center. If you have large internal motions, the average structure will
be correspondingly distorted. Also, if you don't RMS fit each
structure to some reference prior to calculating the average structure
you may get contributions from rotational/translational motion in the
average.
Because average structures may be distorted, this can mess with the
simple bond searching algorithms in programs like VMD, leading to even
stranger-looking structures. So when loading average PDBs it's often
better to first load your topology, or better yet save average
structures in a format that contains bond info like mol2 (only
possible with cpptraj).
Hope this helps,
-Dan
>
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Aug 05 2014 - 06:00:02 PDT
