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

Abelak, Kavin kabelak at rvc.ac.uk
Fri May 1 13:30:43 CEST 2015

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.


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

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