[gmx-users] DNA-ligand interactions with AMBER

[Paulo Netz]

Dear Gromacs users

I am simulating the interactions between ligands and DNA
using GROMACS with the AMBER force field, as implemented with
the AMBER PORT for GROMACS. Simulating DNA is actually
very easy with this protocol, but for the ligand some
problems arise. Until now we are constructing the
topology manually, but this became complicated for large
ligands. What is the best way to construct ligand
topologies with AMBER parameters, for using with GROMACS,
provided that we DO NOT have the AMBER package?

Thank you very much in advance.

Paulo Netz