VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Jul 17 2013 - 14:54:00 CDT

Francesco,

The ParamChem web-server is a good resource to assign CGenFF/CHARMM36 atom types and to determine what other bonded terms require parameterization/refinement. Carefully note the penalty values associated with the output. Molefacture is mostly used for generating PSF/PDB file pairs that are the required input for ffTK. The build-in atom typer in Molefacture is a bit out-of-date and uses the UFF, which is quite different from CHARMM; you should manually enter in the type information based on the ParamChem output instead of using whatever Molefacture assigns.

Regards,
Christopher Mayne

On Jul 17, 2013, at 10:14 AM, Francesco Pietra wrote:

> Hello:
> I wonder whether CGenFF can be of any help to set up parameters for a
> new ligand of a protein with FFTK for NAMD.
>
> As there are atom types not comprised directly in CHARMM FF v 27, I
> used CGenFF before going to MOLEFACTURE, however getting atom types
> for CHARMM ff version 36.
>
> I know there is a flag for NAMD to use CHARMM mode dealing with L-J,
> however, has v27 been combined with v36? Can them be used for the same
> run?
>
> thanks
> francesco pietra