[gmx-users] Heme params for amber99sb-star-ildn

[Abelak, Kavin]

Dear Gromacs users,

I am looking for ready made heme B parameters for use in md runs of CYP enzymes.

Heme is defined in Gromos54a7 ff, but I am looking for a definition for amber99sb-star-ildn as I am planning to use QM charges pre-calculated (and published  -  doi: 10.10002/jcc.21922) for the amber ff. Also, the Cys-S to Heme-Fe bond is not defined within gromos, which makes treating the CYP and Heme as one entity impossible.

So far, I have (with help):
defined a heme and Cys within aminoacids.rtp
added the heme and Cys to residuetypes.dat
added required lines to specbond.dat
defined hydrogens in aminoacids.hdb
created atom types in atomtypes.atp
created corresponding non-bonded params in ffnonbonded.itp
created most of the missing bonds/angles/dihedrals in ffbonded.itp

I seem to be stuck on improper dihedrals. If anyone has done similar work and has files they are willing to share, I’d be most grateful.

Thanks,
Kavin

-----------------------------
Kavin Abelak
PhD Student
Dept of Comparative Biomedical Sciences
Royal Veterinary College
kabelak at rvc.ac.uk



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