[gmx-users] [Fwd: Loss of bonds in HEME iron after pdb2gmx]

saradas at ncbs.res.in saradas at ncbs.res.in
Wed Dec 10 07:59:50 CET 2008

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.
Graduate student,

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