[gmx-users] Protoporphyrin parameters & PRODRG

David van der Spoel spoel at xray.bmc.uu.se
Fri Mar 22 02:04:14 CET 2002

On 21 Mar 2002, Michel Fodje wrote:

>Hello everyone,
>I would like to do some simulations with protoporphyrin IX. To get
>parameters, I added an entry in "ffG43a1.rtp"  and "ffG43a1.hdb" based
>on the HEME entry -- basically, I removed all the bonds and angles that
>involved FE. I confused though, how to assign partial charges to the
>central Nitrogen atoms. In HEME these atoms have -0.1 charge.
>Using PRODRG, i get a topology with Zero charge on the nitrogens even
>though no hydrogens have been added to these atoms. Of course I could
>add them manually. Or should I leave them out, and distribute the -2
>charge equally to all four nitrogens?  
Best option would be some quantum calculations. The system is rather 
symmetric I assume.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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