Hi everyone,
I need to perform MD simulations on a large number of protein-ligand docked complexes (88 or more).
Previously, I used Swiss Param website to generate ligand topologies and CHARMM force field but I faced many errors related to topology files.
Please suggest me the best Gromacs-based protocol to conduct MD simulations, using any combination of server, force field, etc.
I would appreciate comprehensive guidance about details.
What are ligand atoms? Did you check AmberTools or PRODRG for AMBER and GROMOS force fields?
https://www.researchgate.net/post/How-to-create-topology-file-for-new-ligand-in-gromacs
You can check this tutorial link for protein-ligand complex simulation given by Lemkul.
http://www.mdtutorials.com/gmx/complex/index.html
For ligand topology preparation you can also use prodrg.
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