[gmx-users] compound-I/II topology, i.e. porphyrin(Fe=O)

Arturas a3arzi at vaidila.vdu.lt
Fri Apr 9 10:36:01 CEST 2004


I want to make a topology file for heme with oxygen atom bound to Fe,
i.e. compound-I/II model of oxireductases. PRODRG server supports N,
C, O, S, P, Cl, I, Br, F atoms only. So PROFRG can not help me. How to
solve that problem.

Should it be done by hand modifying standart heme tolopogy ? What are
parameteres for >Fe=O fragment ?

Any tricks and advises.


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