[gmx-users] HEME topology

Shozeb Haider shozeb.haider at pharmacy.ac.uk
Thu Sep 25 17:45:28 CEST 2008


I am trying to simulate HEME in a water box. I generated HEME topology 
based on the parameters in the ffG43a2.rtp file. When I run a short 
burst of unrestrained dynamics, it does not remain planar. I understand 
that there might be some buckling but not to the extent that I am 

My questions is - Do I need to add some more parameters other than the 
default ones in the .top file ? (Impropers and Dihedrals already exist 
with planar flags)

Also is there some heme topology in the public domain that I can compare 
my parametrisation with ?

Many thanks

Shozeb Haider
The London School of Pharmacy

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