Atom types equivalence between CHARMM36 and AMBER99bsc1

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No

Hi all,

I parametrized a new ligand with FFTK to be used in a DNA/ligand simulation. After a comparison between CHARMM36 and AMBER99bsc1 of the DNA system without the ligand, the last reproduced better some experimental features. I used the cgenff_charmm2gmx_py3_nx2.py script to convert my parameters obtained with FFTK into GROMACS format and units. Now, I have to change all CHARMM36 atom types to AMBER atom types, but the equivalence is not obvious. Ex., NG2R50 CG2R51, NG2R50 CG2R53, and NG2R51 CG2R53 bonds in CHARMM36 are defined as NA CC in AMBER. Each bond has slightly different values of b0 and kb.

It is there any recommendation or tool to define this equivalence?

Thanks in advance,
-Yasser

2

You can’t convert a topology parametrized with one force field to another force field. CHARMM and AMBER use different conventions for QM methods, charge assignment, etc. If you want to use AMBER, parametrize the molecule with AMBER (antechamber).

3

Thanks for the reply.