Avijit,
The carbons in the vinyl side chain of the heme are no longer sp2
hybridized in cyt c, since the ligating reaction is essentially an
addition of S-H across the double bond, giving sp3 carbons. You need to
modify the heme parameter file so as to reflect this. The residue type
for both the iron ligand and the ethylene group Cys should be modified
as well, the axial Fe ligand is CYM. Not sure what would be best for
the covalent link Cys, maybe whatever is used for disulfide bridges?
Tom P.
On 8/5/17 3:56 AM, Avijit Rakshit wrote:
> Andrew
>
> But those examples are for cytochrome P450. There HEM gr is not covalently
> bonded to S of CYS residue. My protein is horse heart cytochrome C where
> sp2 carbon of porphyrin ring is making covalent bonds with S of cystine of
> main protein chain. So it is not getting the parameters for that bond.
>
> On Sat, Aug 5, 2017 at 1:13 PM, Andrew Schaub <aschaub.uci.edu> wrote:
>
>> Avijit,
>>
>> I'm not sure about the Bryce parameters. I would recommend one of two
>> options.
>>
>> 1) [Less work] Use the Shahrokh heme parameters if your heme is coordinated
>> to a cysteine. Those parameters can be found at:
>>
>> J Comput Chem. 2012 Jan 15; 33(2): 119–133.Published online 2011 Oct 14.
>> doi: 10.1002/jcc.21922
>>
>> They'll be listed in the S.I.
>>
>> 2) [More work, requires a QM program] Follow the MCPB Heme tutorial:
>> http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm and
>> derive
>> your own parameters.
>>
>> Personally I just follow the second option as it gives you more control
>> over system setup. Good Luck!
>>
>> Best Regards,
>>
>> Andrew
>>
>>
>>
>>
>> On Sat, Aug 5, 2017 at 12:29 AM, Avijit Rakshit <avrakjnu.gmail.com>
>> wrote:
>>
>>> Hello all,
>>>
>>> I am trying to parametrize HEM group of horse heart cytochrome C where
>> the
>>> porphyrin ring is covalently bonded through a sp2 carbon to the S atom of
>>> Cystine side chain. As suggested from previous Amber mailing lists I took
>>> the heme_all.inpcrd and frcmod file from Bryce group page
>>>
>>> http://research.bmh.manchester.ac.uk/bryce/amber
>>>
>>> After connecting the HEM group with S atom of CYS I am not getting the
>>> following parameters.
>>>
>>> Could not find bond parameter for: S - CY
>>> Could not find bond parameter for: S - CY
>>> Building angle parameters.
>>> Could not find angle parameter: S - CY - CB
>>> Could not find angle parameter: S - CY - CX
>>> Could not find angle parameter: 2C - S - CY
>>> Could not find angle parameter: S - CY - CX
>>> Could not find angle parameter: S - CY - CB
>>> Could not find angle parameter: 2C - S - CY
>>> Building proper torsion parameters.
>>> ** No torsion terms for 2C-S-CY-CB
>>> ** No torsion terms for 2C-S-CY-CX
>>> ** No torsion terms for 2C-S-CY-CX
>>> ** No torsion terms for 2C-S-CY-CB
>>>
>>> I think here CB,CY and CX are sp2 hybridized carbon from the porphyrin
>> ring
>>> and S is Sulphur atom of CYS group from main protein chain.
>>> Can anyone please suggest me how to get those parameters ?
>>>
>>>
>>> --
>>> With regards
>>> ---------------------
>>> Avijit Rakshit
>>> Ph.d student
>>> School of Computational and Integrative Science
>>> Jawaharlal Nehru University
>>> New Delhi
>>> 110067
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>> --
>> Andrew Schaub
>> Graduate Program in Chemical & Structural Biology
>> Tsai Lab, http:///www.tsailabuci.com/ <http://www.tsailabuci.com/>
>> Luo Lab, http://rayl0.bio.uci.edu/html/
>> University of California, Irvine
>> Irvine, CA 92697-2280
>> 949-824-8829 (lab)
>> 949-877-9380 (cell)
>> aschaub.uci.edu <http://www.linkedin.com/pub/andrew-schaub/9a/907/382/>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Sat Aug 05 2017 - 05:30:02 PDT
