VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 28 2007 - 16:12:02 CDT

Hi,
  I've bounced your queries to Jan Saam, the author of Paratool,
hopefully he'll have a few minutes to answer your questions, though I
know he is quite busy so please be patient.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 28, 2007 at 05:57:05PM +0200, Karol Kaszuba wrote:
> Hello !
> I have some questions about paratool plugin and ligand parametrization:
> 1) There is an option which is named "Determine RESP charges".
> Does it an equivalent of RESP procedure in AMBER - I mean automated
> charge fitting based on ESP?
> 2) I would like to optimize a geometry of my molecule and calculate ESP
> in GAMESS?
> As far as I know actually paratool plugin can read only GAUSSSIAN
> log file?
> Does anyone know a tool which can convert a GAMESS output log (at
> least ESP calculation output) to GAUSSIAN log - maybe BABEL?
> 3) I am able to derive all parameters for my ligand based on topology
> file - point charges too.
> So my questions are:
> a) Do I have to calculate charges de novo (based on ESP) ?
> b) Can I use these "topology" charges for docking studies ?
> Thank you in advance,
> Regards,
> Karol 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078