[gmx-users] Simulation of the HEM-containing proteins

[James Starlight]

Dear Gromacs users!


I want to simulate Cytochrome C in complex with HEM using NMR full-atom
structure of that protein as the starting conformation and charm36 force
field's parameters.

in the charm36 ff I've found parameters for HEM but I have not found params
for the hydrogens (in the aminoacids.hdb file) as well as definition of the
HEM as the part of the protein in the residuetypes.dat ( including
connection to the rest of polypeptide chain ).

So during pdb2gmx parametrisation I've obtained errors like

WARNING: atom HA is missing in residue HEME 105 in the pdb file
         You might need to add atom HA to the hydrogen database of building
block HEME
         in the file aminoacids.hdb (see the manual)


WARNING: atom HB is missing in residue HEME 105 in the pdb file
         You might need to add atom HB to the hydrogen database of building
block HEME
         in the file aminoacids.hdb (see the manual)


WARNING: atom HC is missing in residue HEME 105 in the pdb file
         You might need to add atom HC to the hydrogen database of building
block HEME
         in the file aminoacids.hdb (see the manual)


WARNING: atom HD is missing in residue HEME 105 in the pdb file
         You might need to add atom HD to the hydrogen database of building
block HEME
         in the file aminoacids.hdb (see the manual)


Have anybody such missing parameters?


James