[gmx-users] NAPDH hopeless

[Virtual Daan]

Sergio

What is wrong with submitting the PDB file as is to the PRODRG server and
switching the "EM" button to OFF? You can use the PATCH instructions (see
FAQ) to add or delete hydrogens at will!

Daan

On Tue, 1 Apr 2003, Sergio Manzetti wrote:

> Its hopeless to use the existing force field data for two reasons: the
> original NADPH PDB file (from a crystal structure) lacks 4 hydrogens
> (acccording to pdb2gmx). Building a PDB of NADPH from scratch presents an
> impossible challenge, where the oritentation of the NADP molecule has to be
> finetuned with the amino acids around it for crucial H.bond network. This
> is not reproducible with the Prodreg server, after generating the topology
> and cuting and pasting it in the protein topology....
>
> I tried to go without the 4 hydrogensm but the NADPH molecule exploded in
> fron of my eyes in ngmx.
>
> I am out of options. This is too tricky, is there a way gromacs can be made
> better to recognize such molecules adn prevent these molecular explosions?
>
> Attached a PDB file illustrating the NADP and its neighbours
>
> Sergio


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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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