[gmx-users] clustering "pdb outsiders"

[Berk Hess]

>From: "Nuno R. L. Ferreira" <nunolf at ci.uc.pt>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] clustering "pdb outsiders"
>Date: Mon, 28 Jun 2004 12:10:48 +0100
>
>Hi *
>
>I've some hundreds of pdbs (conventional format) that came out from a 
>docking
>calculation.
>
>My aim is to analyze these structures, using g_cluster, to find out how's 
>the
>cluster distribution.  I don't know of any other soft. that can do this, so 
>I
>pointed my batteries to gmx.
>
>Some thoughts that ocurred me ...
>
>1- First I have to build a tpr file for  one of the input pdbs (they 
>contain
>only regular aminoacid residues).  The input pdbs have 3 chains, and each 
>one
>is also broken in 3 pieces.   I tryed to build a topology using opls f.f. 
>and
>I was successful.  Just have to figure out how to resolve 2 long bond
>warnings, for each chain (possibly the bond between the chain broken 
>parts).

g_cluster does not require a tpr, you can also supply a pdb file with -s.

But do check the bux report and fix of last week by Roman Affentranger.
The average rmsd's and the middle structures are reported incorrectly
by g_cluster, the clustering itself is correct though.

Berk.

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