[gmx-users] Protein-ligand opls ff

Jonathan Saboury jsabou1 at gmail.com
Tue Feb 21 18:56:42 CET 2017

I'm very inexperienced, so probably shouldn't be giving advice, but I think
the below is correct :)

Justin Lemkul has made many tutorials that have been invaluable to me.
Below is his tutorial on how to prepare such a system using the GROMOS96
43A1 force field. (This can be changed to OPLS-AA/L all-atom force field
during the "gmx pdb2gmx -f 3HTB_clean.pdb -o 3HTB_processed.gro -water spc"


Since you already have your ligand .top file you just need to copy and
paste the ligand.itp line from that .top to your new one.

Good luck!

- Jonathan

On Tue, Feb 21, 2017 at 9:27 AM, Chetan Puri <chetanpuris at gmail.com> wrote:

> I want to do a protein ligand MD in GROMACS using OPLS-AA force field,
> So can someone suggest how to proceed with ligand topology file.
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