[gmx-users] clustering "pdb outsiders"

[Andrea Carotti]

You can take a look here
http://neon.chem.le.ac.uk/nmrclust/protocol.html

Bye
Andrea
----- Original Message ----- 
From: "Nuno R. L. Ferreira" <nunolf at ci.uc.pt>
To: <gmx-users at gromacs.org>
Sent: Monday, June 28, 2004 1:10 PM
Subject: [gmx-users] clustering "pdb outsiders"


> 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).
>
> 2- Concatenate all the pdbs, to have a kind of trajectory, ready to be fed
up
> into g_cluster (easy thing to do).
>
> I think I have to change the nomenclature of the input pdbs, to meet the
> nomenclature stored under the produced .tpr file (residue and atom names I
> mean).
> But this is rather difficult to do, cause not only I have to change some
> residue names (like LYS --> LYSH, or HYS --> HISA), atom names (like ILE
HD11
> --> ILE HD1), but also I suppose that I have to change the residue number,
> cause pdb2gmx joins all those broken pieces, renumbering them.
>
> Any suggestions ?
>
> Best regards,
> Nuno
>
>
>
> -- 
> **********************************************
> Nuno Ricardo Santos Loureiro da Silva Ferreira
> Grupo de Química Biológica
> Departamento Química
> Universidade de Coimbra
> Portugal
> www.biolchem.qui.uc.pt
> **********************************************
> "Do not worry about your difficulties in maths.
>  I can assure you that mine are still greater."
>                                    emc2
>
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