Molecular Dynamics Simulation of MetalContaining Ligands?

05 May 2019 1 6K Report

I'm currently working on metallic ligands (transition metals/complexes as ligands). For their MD Simulation, how to generate topology for ligand, kindly help?

Prasanth G.

Hello,

You could use antechamber from ambertools (freely available).

Tutorial here - http://ambermd.org/tutorials/basic/tutorial4b/

You can proceed to do the simulations as mentioned in the tutorial or you could use the tool "acpype" to convert the prmtop and inpcrd files to the GROMACS equivalent ones.

P.S: Kindly use the appropriate AMBER forcefield in GROMACS.

Hope it helps.

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