Protein-ligand Molecular dynamics using gromacs


#1

How to prepare hybrid forcefield in case of protein ligand simulation


#2

Hello and sorry for the long delay before answering.

For simulating ligands that have not been parameterized for your force field, you need to perform the step of obtaining the parameters yourself.
Some hints can be found here (http://manual.gromacs.org/documentation/current/user-guide/faq.html#parameterization-and-force-fields) and here (http://manual.gromacs.org/documentation/current/how-to/special.html#parameterization-of-novel-molecules).
Please be aware that the process of preparing a new residue for a simulation and its validation can be time consuming and difficult, even for expert users.

Cheers
Paul