VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Mon Aug 27 2007 - 03:56:34 CDT

Dear Jacob and Francesco,

I am about to finish my PhD thesis and have virtually zero time to do
anything for Paratool these days.
This should all change in November where I will start dedicating most of
my time to Paratool. I know that I had promised this log time before
but, well, there are so many things that can distract and dely your work...

There is no button you missed after the singlepoint calculation. This is
the point where the manual work of parametrization begins. I order to
make this semi-automatic I have to totally restructure the inner
workings of Paratool. Any other additions or fixes are a waste of time.
However, I'm hoping for relative fast success after November. Jacob,
since I have your files, you'll be one of my official test cases.

Sorry for not being more helpful at the moment,
Jan

Francesco Pietra schrieb:
> 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
>>
>>
>>
>
>
>
>
> ____________________________________________________________________________________
> Pinpoint customers who are looking for what you sell.
> http://searchmarketing.yahoo.com/
>
> 

-- 
---------------------------
Jan Saam
Institute of Biochemistry
Charite Berlin
Monbijoustr. 2
10117 Berlin
Germany
+49 30 450-528-446
saam_at_charite.de