[gmx-users] questions about PRODRG

[Daan Virtual]

Hi Ruben

The resolution as such as nothing to do with PRODRG, but more with the
quality of the electron density map that was used to build a model for the
ligand.
I would very strongly recommend you spend 5 minutes drawing your ligand
in the funny C-C=C system - in terms of reliability this is superior to
using coordinates as input. If you have to use coordinates - go for the
CSD ones.

cheers

Daan

On Fri, 22 Nov 2002, Ruben Martinez Buey wrote:

>  Hi everybody!!
>
> If I want to generate a topology with PRODRG, what is better?? taking the coordinates from the crystal structure of the small molecule (from the Cambridge database),
>
> or taking the coordinates of the ligand (the one in the binded conformation) from the crystal structure of the complex protein-ligand. Have I to take into account the resolution to choose one of theese??
>
> Another question: coordinates from the crystal structure of the ligand (from the ligand-protein complex ) at medium resolution (3.0-3.5 A) are OK for PRODRG
>
> or does it need higher resolution?? I mean, is the resolution a so critical factor for PRODRG?? (I read in the paper for PRODRG that it was, but I ask how big is it??)
>
> Thans in advance for your kind attention,
>
> with best regards,
>
> Ruben
>
> ___________________________________________
>
> Rubén Martínez-Buey. PhD student
> Protein Function and Structure Dept. Lab. 352
> Centro de Investigaciones Biológicas (CIB-CSIC)
> C/ Velázquez, 144  28006  MADRID
> Tlf: +34-91-561 18 00 ext. 4380
> ___________________________________________
>
>
>


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Dr. Daan van Aalten                    Wellcome Trust CDA Fellow
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk

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