[gmx-users] NAPDH hopeless

David van der Spoel spoel at xray.bmc.uu.se
Tue Apr 1 16:57:01 CEST 2003

On Tue, 2003-04-01 at 16:41, 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

first off, the names in your pdb file are f*cked up. make sure they are
second, pdb2gmx takes the NADP for an NADH, no wonder it won't work.
Rename the NAD in your pdb file to NAP, and do also rename the NADP
resiudue in the appropriate rtp file (ffgmx.rtp or ff43a1.rtp) and hdb
file to NAP.

Try again.

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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