Dear Sarada,
You need to paramterize the Cysteinyl ligand manually. There are a
variety of references in the literature that provide reasonable
energies. Below is a pretty good reference.
Best wishes,
Art
1. Oda, A., Yamaotsu, N., and Hirono, S. (2005) New AMBER force field
parameters of heme iron for cytochrome P450s determined by quantum
chemical calculations of simplified models, J. Comput. Chem. 26,
818-826.
On Dec 9, 2008, at 10:59 PM, sara...@ncbs.res.in wrote:
Hello,
I am working with the simulation of cytochromeP450. There is a bond
between the S of cystine and FE of HEME. During the grompp step I get
warnings that there is no default bonds/angles/dihedrals all
pertaining to
the cystine-heme bond. In the archives it was mentioned that these
values
must be taken from ffG**bon.itp and included in the topology file.
However
in the ffG**bon.itp file, the bonds/angles mentioned seem to be
between S
of CYS and the carbon atom of HEME. For eg,
; bond-, angle- and dihedraltypes for specbonds:
[ bondtypes ]
S S 2 gb_33
NR FE 2 gb_32
; cystine - heme link (is CR1-S, use CH2-S):
S CR1 2 gb_30
Should not the cystine - heme link have FE insteadof CR1? I understand
that I am missing some crucial point here. Kindly help.
Thanks.
Sarada
Graduate student,
NCBS,
Bangalore
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