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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
