Re: [gmx-users] on md of protein-ligand complex

Hi, Take a look at acpype or FESetup. Those are automated tools that will do the conversion to gromacs compatible files. Dear All, For a MD of a protein-ligand complex, I intend to use AMBER99SB-ILDN protein force field for the protein part. If I use the antechamber (for GAFF force field) to pro

Re: [gmx-users] on md of protein-ligand complex

See PRotein-Ligand tutorial everything is explained well, acpy you can use to get gromacs topology for amber! though ambertools -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www

[gmx-users] on md of protein-ligand complex

Dear All, For a MD of a protein-ligand complex, I intend to use AMBER99SB-ILDN protein force field for the protein part. If I use the antechamber (for GAFF force field) to produce the ligand top file and gro file, can GROMCS accept this kind of antechamber produced ligand files for MD? Brett