[gmx-users] heme group in protein

[Maija Lahtela]

Dear Gromacs Users,

I am studying a protein containing heme group. I checked that heme is
included ffgmx.rtp file and FE is ffgmx.atp. 
Are there a topology file for heme available gromacs or should I generate
it ( I got the error message in pdb2gmx that residue 'HEME' not found in
residue topogy database).  I tried to make topology file for heme taken
from pdb-file using PRODRG webserver but the error was that PRODRG does
not model bond between non-carbon atoms.   

How I should proceed with heme group in order to able do MD simulations
with gromacs ?

Yours,
Maija Lahtela-Kakkonen

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Maija Lahtela-Kakkonen, 
Research Scientist
Department of Pharmaceutical Chemistry
University of Kuopio
P.O.Box 1627, FIN-70210 Kuopio, FINLAND
tel: +358-(0)17-162462, fax:+358-(0)17-162456
e-mail: mlahtela at csc.fi
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