VMD-L Mailing List

From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Jul 17 2013 - 15:27:27 CDT

Francesco,

Molefacture uses localized bond orders and oxidation states; however, this is more to detect valencies for visualization and the "add all hydrogens" function than any sort of charge calculation or complex aromaticity detection. Charges are assigned according to a fixed point charge model. As far as I'm aware, these charges are computed using external dependencies, and Molefacture just assigns them to a particular atom.

Regards,
Christopher Mayne

On Jul 17, 2013, at 12:48 PM, Francesco Pietra wrote:

> In this connection I also wonder how molefacture treats pyrrole,
> either quasi-aromatic or localized C=C, in order that the total charge
> is zero.
> Thanks
> francesco pietra
>
>
> ---------- Forwarded message ----------
> From: Francesco Pietra <chiendarret_at_gmail.com>
> Date: Wed, Jul 17, 2013 at 5:14 PM
> Subject: vmd-l: FFTK and CGenFF
> To: vmd-l_at_ks.uiuc.edu
>
>
> 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