VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Aug 21 2007 - 10:29:41 CDT

I join Jacob's wish. Perhaps, however, my aim (to treat by MD very large, non
polymeric organic molecules) poses too hard problems to such tools as Paratool
or Antechamber. I have tried extensively the latter because I have Amber9 (and
VMD) installed. At any event, I would be interested to run a full session of
Paratool. Jan, I have seen your most intersting paper on PNAS.

francesco

--- Jacob Poehlsgaard <mail_lists_at_hardcoil.net> wrote:

> Jan Saam wrote:
>
> > I wonder if actually ever anybody other than me was able to do some
> > thing useful with Paratool. My assumption is that everybody who tried it
> > got stuck at one or the other point and gave up.
>
> That's where I'm at currently. One thing that would REALLY help me
> would be a short example of running a small molecule through the
> process. Nothing too extensive.
> I'm currently stuck after the singlepoint calculations, and I don't
> know if the next steps aren't implemented in the current version, or if
> I just need to press a button I'm missing.
>
> Jacob
>
>

       
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