Hi,
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
observing.
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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