[gmx-users] Atom types comparison between CGenFF and Charm36FF

[Mohsen Ramezanpour]

Dear Gromacs Users,

I am trying to parameterize a molecule in Charmm36FF.

As part of this molecule, there is a "neutral trimethylamine nitrogen" and
its protonated case. i.e. C-N-C(2) and C-N(H)-C(2), respectively.

To have some idea about the appropriate atom types, I first used the
GAAMP server.

Here are the assigned atom types by GAAMP (based on CGenFF force field):


*For Neutral case:*
NG301 for N,
CG3AM0 for two methyl group connected to the N, i.e for bolded Carbons in
C-N-*C(2).*
HGA3 for each Hydrogen atom in CG3AM0 methyl groups,
CG321 for the carbon atom connecting the NC(2) to the rest of molecule.
i.e. for bolded Carbon in *C*-N-C(2),
and HGA2 for the Hydrogen atoms connected to CG321.
###############################

*For Protonated case:*
NG3P1 for N,
CG334 for two methyl group connected to the N, i.e for bolded Carbons in
C-N(H)-*C(2).*
HGA3 for each Hydrogen atom in CG334 methyl groups,
CG324 for the carbon atom connecting the NC(2) to the rest of molecule.
i.e. for bolded Carbon in *C*-N(H)-C(2),
and HGA2 for the Hydrogen atoms connected to CG321.
################################

Now, I want to find the best equivalent atom type in Charmm36FF for each
case.

For the protonated case, I think it is easier as it is something between PE
and PC lipid headgroups. For the neutral case, however, it is difficult to
find similar atom types in Charmm36.

My approach was to check the LJ and bonded parameters for the assigned atom
types (which are in CGenFF) and find the atom types in Charmm36 with the
exact same values. Although possible for some cases, but there are many
problems with this approach:

1) the exact values are not found in Charmm36FF.
2) If it is found, there are a lot of parameters missing in the Charmm36FF
force field. Not all the bonds, angles, and dihedrals are defined in
Charmm36FF.

Thanks in advance for any comment or suggestion.

Cheers,
Mohsen





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