VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed Jan 23 2013 - 14:26:59 CST

What do you mean by "VMD Auto-parametrization tool"? Paratool? You should use fftk (forcefield tool kit) - but make sure to get the latest version of VMD (possibly one of the alpha builds even). The former, paratool, needs to be removed from the menu.

On Jan 23, 2013, at 2:39 PM, Roy Fernando wrote:

> I am trying to use VMD Auto-parametrization tool to create topology and parameter files for the active site of Superoxide Dismutase (SOD).
>
> The active site contains a FE ion covalently bonded with three nitrogen atoms of three HIS residues, one oxygen atom from a ASP residue and an oxygen atom form a solute (water) molecule.
>
> I separated the active side and wrote a pdb file to use as the base molecule. I am now stuck in the attempt to determine the partial charges to the active site atoms. Can someone please suggest something for met to hang on to? IS there a standard set of values I can use and optimize.
>
> Thanks in Advance!
>
> Ajith
>
>