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

Arthur Roberts aroberts99163 at yahoo.com
Sat Dec 13 04:21:02 CET 2008

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,

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,  

On Dec 9, 2008, at 10:59 PM, saradas at 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,
> Bangalore
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