Web server generates gromos-based parameters for molecular dynamics in drug-like molecules, suggesting improved simulations.
A web-server to generate GROMOS (force field)-compatible parameters for large organic drug-like molecules and complex natural products is presented. The web-server GROLIGFF (https://groligff.net) provides force field topology and parameters that can be used to perform Molecular Dynamics (MD) simulations, Linear Interaction Energy (LIE) calculations and Alchemical Free Energy (FE) calculations. The force field description is generated using a rule-based method combining the GROMOS 54A7 biomolecular force field for bonded and van der Waals parameters with a Bond Charge Increment protocol for partial atomic charges. The output parameters can be used with GROMACS, GROMOS and AMBER (with gromos2amber conversion) programs with a recommended single range 1.4 nm cut-off for non-bonded interactions.
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Alpeshkumar K. Malde (2025) studied this question.
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