GROMOS(force field)-compatible parameters for Large Organic Drug-like Hereromolecules and Complex Natural Products to facilitate Molecular Dynamics (MD) simulations, Linear Interaction Energy (LIE) and Free Energy (FE) calculations in Computational Drug Design.

It is primarily designed for large molecules where ab inito or DFT calculations are computationally forbidding. The force field description is generated using a rule-based method combining the Gromos54a7 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 and GROMOS MD programs with a recommended single range 1.4 nm cutoff.

Input - a QM / MM geometry optimized 3D coordinates file of the desired protomer/tautomer with all Hydrogen atoms in pdb, mol, sdf, mol2 or pdbqt format

Molecules containing - C, N, O, S, P, F, Cl, Br, I - elements and upto 500 atoms are supported

Some atoms may be renamed while the order of atoms is retained

Garbage-in-garbage-out

Output - United-atom building block files (i) MTB (gromos), (ii) ITP (gromacs), (iii) corresponding PDB coordinate file and (iv) a modified 54A7_LIG.ifp (gromos) file containing additional bonded parameters.

Citation: Malde AK. GROLIGFF - GROMOS force field compatible parameters for Heteromolecules. ChemRxiv 2024. doi:10.26434/chemrxiv-2024-m555w-v2

Disclaimer: User is advised to treat these parameters with discretion and to perform additional validation tests for specific application if required. We do not accept any liability for how the parameters may be used. No uploaded data is stored for more than few minutes.

Acknowledgment: Dr. Tom Litfin for fascilitating the web interface.

GROLIGFF - GROmos-compatible LIGand Force Field - 1.0