[gmx-users] NADP inferno

[David van der Spoel]

On Mon, 2003-04-07 at 17:00, Sergio Manzetti wrote:
> Hi all, in regard with NADP in simulation with this protein I have, after 
> taking Daan's and Davids advices into account decided to generate the PDB 
> of it through PRODREG, then simulate it in vacuum, then in water and then 
> with the protein.
> 
> The first errror in this path is when using PDB2GMX (I use the PDB with 
> polar hydrogens only) :

first error is that you need not run pdb2gmx if you get your topology
from PRODRG

> 
> Fatal error: Atom NBO in residue NADP 1 not found in rtp database
>               while sorting atoms
> 
> 
> The atomic nomenclature from Prodreg is incorrect! ..using Gromos ore 
> Gromacs force field
> 
> Stuck!
> 
> Sergio
> 
> 
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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