GROMACS version: 2022.2
GROMACS modification: No
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Is it possible to simulate two ligands or two compounds using gromasc? This simulation does not involve proteins at all, I want to see the stability of the bond between the two compounds. If so, is there a tutorial I can follow? Thank You
Hi, not sure if this late reply is still useful at this point, but have you taken a look at GROMACS tutorial 5 on the protein-ligand complex? Part of that tutorial involves creating topology files for the ligand then putting it in the same simulation as the protein, it might be a good starting point if you’re trying to figure out how to take 2 separate compounds and placing them into a single topology file.
Thank You, I really appreciate your advice. I have performed the GROMACS procedure you mentioned, but it was challenging because it required editing force fields and creating specific parameters. I am not skilled in that area and do not have time to do it myself. Then last month, I could simulate those two molecules using tleap from Amber and converted the Amber format back to GROMACS. Here are the commands I used. Hopefully, someone reading this in the future will find them helpful GitHub - purnawanpp/gmx_2compound: This tutorial to simulate two compound in GROMACS