Parametrize new ligands for AMBER and CHARMM

      For those who need to parametrize new ligands, there is a new alternative VMD pluggin, named Paratool,  to do so. It works for both AMBER and CHARMM, but has been specially designed for the latter one.

      Paratool provides a graphical interface for force field parametrizations of molecules that are not contained in your force field. It is designed to generate CHARMM or AMBER compliant parameters 

    The plugin helps you to generate the molecule or the moleular fragment that should be parametrized and to set up the necessary quantumchemical calculations (you'll need Gaussian, later versions will also support GAMESS). Paratool reads the logfiles of the QM simulations, computes force field parameters for bonds, angles dihedrals and impropers by transforming the Hessian into internal coordinates and converting all values into units based on kcal/mol, Å and degrees. You can assign atom types and the corresponding VDW parameters from a list of already existing types or generates new types (all chemical elements H - Rn supported). The charges can be determined using restricted electrostatic potential fitting RESP (AMBER style) or CHARMM style charges using their supramolecular approach which requires another Gaussian calculation.

     Paratool generates input for all necessary external programs collects and compiles all the necessary data, organizes and displays them neatly in lists and projects them onto your molecule in VMD. Finally it will write the topology and parameter files you'll need to build the molecule using psfgen and run your simulation in your favourite simulation package, e.g. NAMD.

     I hope it may help you.

     For additional help, look at: