[gmx-users] ligand-protein interaction using gromacs

Dear all, I'm trying to study the interaction between NADH and a protein. And because the parameters for NADH have been developed in amber99 and amber94 force fields, so I just used the contributed parameter files for my simulation. The coordinates I got from docking results. I made my

Re: [gmx-users] ligand-protein interaction using gromacs

Quoting #NGUYEN CONG TRI# [EMAIL PROTECTED]: Dear all, I'm trying to study the interaction between NADH and a protein. And because the parameters for NADH have been developed in amber99 and amber94 force fields, so I just used the contributed parameter files for my simulation. The

Re: [gmx-users] ligand-protein interaction using gromacs

Regarding amb2gmx.pl, it should work for converting whole systems from Amber, but this may depend on the box geometry you are using. In particular I think it is OK with cubic boxes but not some of the more fancy geometries. The other option is just to convert your protein+ligand and solvate using