[gmx-users] Re: gmx-users Digest, Vol 56, Issue 43

[saradas at ncbs.res.in]

Dear Art,
Thanks a lot for the reference.
Regards,
Sarada

>> Message: 5
> Date: Fri, 12 Dec 2008 19:21:02 -0800
> From: Arthur Roberts <aroberts99163 at yahoo.com>
> Subject: Re: [gmx-users] [Fwd: Loss of bonds in HEME iron after
> 	pdb2gmx]
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <81B152BC-BB35-4CF2-A9E5-736C20E89E48 at yahoo.com>
> Content-Type: text/plain; charset="us-ascii"
>
> 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, 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,
>> NCBS,
>> Bangalore