VMD-L Mailing List

From: Jan Saam (jan.saam_at_charite.de)
Date: Mon May 28 2007 - 18:51:57 CDT

Hi Karol,

> 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?

Try it out! It's RESPtool is a graphical fromtend to RESP, The
calculations are performed by RESP itself and you must have it installed
on your system.
RESPtool is not fully automatic but it makes it easier to understand what
you are actually doing in RESP and gives you a more convenient control
over the program.
>
> 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?

As far as I know there's no such tool.

>
> 3) I am able to derive all parameters for my ligand based on topology file
> - point charges too.

Very good!

> So my questions are:
> a) Do I have to calculate charges de novo (based on ESP) ?
I'm more experienced with CHARMM that AMBER but I think the same rule
applies:
If you were able to derive your parameters from the modelcompounds of the
force field you probably don't need de novo RESP/ESP charges. But careful:
if you rip model compounds apart and/or you encounter non-integer molecule
charges something is wrong or you need new charges.

> b) Can I use these "topology" charges for docking studies ?
AMBER charges should be fine for docking. You might want to take a look at
"autodock", they use AMBER charges for docking as far as I remember.

Good luck,
Jan
>
>
> Thank you in advance,
> Regards,
> Karol
>
>