VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 24 2013 - 10:54:14 CST

Hi,
  Just FYI, the old paratool plugin still exists in the current test
versions of VMD, but had already been "hidden" from the menus for quite
some time. I assume that Roy/Ajith is using an older VMD version since it's
still shown in his version.

Cheers,
  John Stone

On Wed, Jan 23, 2013 at 03:26:59PM -0500, JC Gumbart wrote:
> 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
> >
> >
> 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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