AMBER99 parametrized molecule in methanol

User discussions
1

GROMACS version: 2019.3
GROMACS modification: No
Dear GROMACS users,
Forgive me if my question may sound naive but I only recently started working with GROMACS and MD simulations in general. I need to simulate a molecule, a non-standard amino acid residue, which has parameters coming from the AMBER99 FF. I was wondering, since I need to do MD simulations of said molecule in methanol box, what would be the best way to go about it?

I see there are OPLS parameters out there, but I am not sure about mixing it up with the AMBER FF of a my solute.

Any help would be greatly appreciated.

Kindest Regards

2

Hi,
up to my knowledge, mixing force fields is usually not so wise if you are not 100% that they are mutually compatible.

Focusing on your problem, you can prepare the input topology and coordinates with AmberTools in AMBER format and convert them in GROMACS format using the amb2gro utility in AmberTools.

Tommaso

3

Hi, yes, that’s indeed the fact that was bothering me.
I already have the topology for my solute, could you explain to me how I would go about using AmberTools ? Sorry, I am very inexperienced.
Thank you in advance,
Leonardo

4

Hi,
for AmberTools you should check the tutorials available on the Amber websites.

When you have your topology and coordinates files in Amber format, you can convert them with the amb2gro_top_gro.py utility implemented in AmberTools.