There is no particular procedure available for running MD of P-L complex in OPLS force field as the provided server ToPolbuild, TopolGen are not available and ligpargen show's error in input files. Any suggestions from where should I learn and implement P-L complex in OPLS force field in GROMACS.
For protein -ligand simulations in gromacs, use charmm36 force field as suggested in Lemkul's tutorial for protein -ligand systems. For ligand topology preparation, you will get stepwise procedure there
Yes, Tanushree Das, I have performed the MD in charmm36ff successfully but I need to work with OPLS ff for my work and the server provided there are not available now for ligand topology generation.
Subhadip Saha, to my knowledge gromos54a7 covers parameters for proteins, nucleotides, sugars etc. Charmm36 for gromacs implemented with Cgenff helps to build the topology and parameters for small compounds (ligands).
To run MD simulations of P-L complexes in the OPLS force field in GROMACS, the Topolbuild and TopolGen servers are unavailable, and the Ligpargen shows errors in input files. To learn and implement P-L complexes in OPLS, consider seeking guidance from bioinformatics forums, tutorials, or researchers experienced in the field. You can also consider trying alternative MD simulation software that support the OPLS force field.
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