[gmx-users] Heme iron - substrate distance

Andrea Hombrecher hombr at pharm.uni-duesseldorf.de
Thu Nov 18 16:08:06 CET 2004

Dear Gromacs users,

when I run a simulation of a heme containing protein with a substrate
bound, the distance between the heme iron and the substrate is always
one Angstrom shorter than in the crystal structure, that I use as
starting structure. Could it be, that the reason for this are the FE
Lennard-Jones parameters? I use the FE LJ-parameters of ffoplsaanb.itp.
When I don't use any LJ parameters, as is the default in ffG43a1nb.itp,
the iron - substrate distance is about the same. Do you have any idea,
how I could improve the iron - substrate distance?


Andrea Hombrecher

Andrea Hombrecher

Heinrich-Heine-Universität Düsseldorf
Institut für pharmazeutische Chemie
Gebäude 26.23.00 Raum 22
Universitätsstraße 1

40225 Düsseldorf

   Tel: 0211-81-12528
   Fax: 0211-81-13847
E-mail: hombr at pharm.uni-duesseldorf.de

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