[gmx-users] Protoporphyrin parameters & PRODRG

[Michel Fodje]

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?  

Any help is highly appreciated.
regards,

Michel

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Michel N. Fodje
Molecular Biophysics,
Lund University, Sweden

phone: +46 46 222 45 13
email: michel.fodje at mbfys.lu.se
web:   http://www.mbfys.lu.se
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