AMBER Archive (2001)

Subject: Fe4S4 cluster

From: Agnes Hahn (agnes_at_ao-hahn.de)
Date: Thu Feb 22 2001 - 10:06:09 CST

Hi folks,

I want to simulate an enzyme that contains an 4 iron 4 sulfur cluster.
For that reason I need parameters (force constants) for bonds Fe-S,
angles Fe-S-Fe, S-Fe-S, and dihedrals Fe-S-Fe-S as well as S-Fe-S-Fe. We
are currently calculating the charges (hopefully that works out).

Also, my enzyme contains a 8-oxoguanine, where carbon C8 is a carbonyl
carbon instead of being bound to a hydrogen. Its neighbouring nitrogen
N7 carries now a hydrogen which it did not before. So carbon C5 is in a
different environment that doesn't consist with the definition of its
name. (I changed the names of C8 and N7, of course.) But there is no
suitible name. I just added parameters in the force field file, which I
would like to correct if you have some better data. I need force
constants for the following: bond N7-C8, angles C8-N7-C5, C8-N7-C5,
C5-N7-H7, N7-C5-C6, N7-C5-C4, dihedrals C8-N7-C5-C6, C8-N7-C5-C4.

Thanks for your help,
Agnes