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
Received on Sat Aug 05 2017 - 00:30:02 PDT
