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
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Received on Sat Aug 05 2017 - 01:00:03 PDT
