AMBER Archive (2008)

Subject: Re: AMBER: Cluster analysis

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Jan 07 2008 - 10:18:22 CST

have you tried doing the cluster analysis in ptraj?
Tom Cheatham had a nice paper recently on clustering using ptraj.
http://dx.doi.org/10.1021/ct700119m

On Jan 7, 2008 11:00 AM, Francesco Pietra <chiendarret_at_yahoo.com> wrote:

> I am trying a cluster analysis with MMTSB, having as guideline tutorial
> A3.
>
> Unlike that, once stripped the environment, I have two molecules, a
> protein and
> its non-polymeric docked ligand. Is any general criterion to adapt to my
> case -
> where the interest is in both molecules - tutorial's conditions for ptraj:
>
> # orient all frames best fit to backbone in NMR structure
> rms first mas :residueX-residueY_at_CA,C,N
>
> taking into account that atom O (oxygen) is of utmost importance for the
> ligand.
>
> Should the analysis be carried out separately for the protein and the
> ligand?
>
> Hope the question is not to cryptic.
>
> The first attempts were unsuccessful, though on simplex examples MMTSB did
> work.
>
> Thanks
>
> francesco pietra
>
>
>
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-- 
===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
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Stony Brook University              E-mail: carlos.simmerling_at_gmail.com
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