GROMACS version: 2020.7
GROMACS modification: No
I’ve been trying to run a MD simulation on a ligand-enzyme (in my case CALB) complex in acetonitrile as solvent but the problem is that I don’t know how to insert my ligand in the active pocket since it’s not a natural ligand for CALB.
Can I make this complex using molecular docking softwares like Glide in Schrödinger suite and then use its results to run my calculation? (Would it be reliable?) I appretiate any help in advance.
P. S. : My main reason for confusion is that I’m using CHARMM36-jul2022.ff for MD simulations but molecular docking softwares like Glide in Schrödinger suite employ FFs like OPLS3
Using output coordinates from a docking software is almost certainly the most reliable way to go. Of course, the quality depends on how accurate the docking poses are, but if there are no experimental structures available then docking poses will give you good starting positions.
That the force fields, for docking and MD simulations, are different should, in most cases, not make a dramatic difference, as long as both are good enough at representing the molecules you are studying. You will need to run energy minimization, and equilibration on your complex, before starting any thorough analyses. Since you need to add water between docking and MD simulations that would be necessary anyhow.