[gmx-users] Heme group with CHARMM27 FF

[Arvind Kannan]

For the benefit of anyone who happens to be Googling the same problem, the following lines inserted into the aminoacids.hdb file will tell pdb2gmx how to correctly protonate the heme.

HEME    16
1       1       HA      CHA     C1A     C4D
1       1       HB      CHB     C4A     C1B
1       1       HC      CHC     C4B     C1C
1       1       HD      CHD     C4C     C1D
3       4       HMA     CMA     C3A     C4A
2       6       HAA     CAA     CBA     C2A
2       6       HBA     CBA     CGA     CAA
3       4       HMB     CMB     C2B     C1B
1       1       HAB     CAB     C3B     CBB
2       3       HBB     CBB     CAB     C3B
3       4       HMC     CMC     C2C     C1C
1       1       HAC     CAC     C3C     CBC
2       3       HBC     CBC     CAC     C3C
3       4       HMD     CMD     C2D     C1D
2       6       HAD     CAD     CBD     C3D
2       6       HBD     CBD     CGD     CAD