Hi Avijit,
The tutorial is just an example, MCPB.py can deal with various bonding situations. I suppose it can work for your system.
Except the tutorial, more information can be checked from the MCPB.py paper: http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674 <http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00674>.
Kind regards,
Pengfei
> On Aug 5, 2017, at 2:56 AM, Avijit Rakshit <avrakjnu.gmail.com> 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
>>
>
>
>
> --
> 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
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Received on Sat Aug 05 2017 - 20:30:03 PDT
