VMD-L Mailing List

From: Karol Kaszuba (karol.kaszuba_at_uwm.edu.pl)
Date: Mon May 28 2007 - 10:57:05 CDT

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