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/>
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Received on Sat Aug 05 2017 - 01:00:02 PDT
