[gmx-users] DNA-ligand interactions with AMBER

[Mark Abraham]

Paulo Netz wrote:
> 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?

You can use AMBER tools like leap and antechamber without a compute 
license for AMBER. See their webpage.

Mark