VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 10 2006 - 19:12:57 CST

You guys have definitely given me some extra entertainment for today :-)

  John

On Fri, Feb 10, 2006 at 05:12:14PM -0800, Warren DeLano wrote:
> Jan,
>
> Wonderful!
>
> Parameterizing small molecules for modeling and simulations is only
> slightly less distasteful to me than cleaning fish -- but don't overlook
> the joys of do-it-yourself home dentistry! Thanks for adding another
> useful tool into the mix, even if it can't chop wood or pop open a brew.
> Happy Friday!
>
> Cheers,
> Warren
>
> > -----Original Message-----
> > From: owner-vmd-l_at_ks.uiuc.edu
> > [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Jan Saam
> > Sent: Friday, February 10, 2006 5:03 PM
> > To: Warren DeLano
> > Cc: John Stone; VMD Mailing List
> > Subject: Re: vmd-l: VMD 1.8.4 beta 11 test version available
> >
> > No Warren,
> >
> > Paratool sweeps the floor, feeds your children but also does
> > undefined things with your wife.
> > Use at your own risk!
> >
> > Well, nevertheless most people will be using it to perform
> > force field parametrizations of molecules that are not
> > contained in your force field. It is designed to generate
> > CHARMM or AMBER compliant parameters (while it is more
> > specialized on CHARMM).
> >
> > Paratool helps you to generate the molecule or the fragment
> > that should be parametrized and to set up the necessary
> > quantumchemical calculations (you'll need Gaussian!).
> > It reads the Gaussian logfiles, converts the number into
> > useful units and computes the bonded parameters. For the
> > charges you can choose between RESP (AMBER style) charges or
> > CHARMM style charges using their supramolecular approach
> > (needs another Gaussian calculation).
> >
> > Paratool compiles all the necessary data, displays them
> > nicely in lists and projects them onto your molecule in VMD.
> > Finally it will write the topology and parameter files you'll
> > need to build the molecule using psfgen and run your
> > simulation in NAMD.
> >
> > Even though Paratool simplifies force field parametrization a
> > lot you'll still need to know what you are doing. I'm
> > currently preparing documentation that will cover the
> > complete parametrization procedure....
> >
> > Jan
> >
> >
> > Warren DeLano wrote:
> >
> > The Paratool extension/plugin is all-new and
> > the author,
> > Jan Saam, hasn't had time to write up
> > documentation just yet.
> > If you're interested in trying it out, you can
> > contact him:
> > http://bioinf.charite.de/biophys/people/saam/
> >
> >
> >
> > Bah! Can your Paratool...
> >
> > Open a six pack of beer?
> >
> > Cut a 2" think wooden board?
> >
> > Be used to remove an infected tooth?
> >
> > Clean fish?
> >
> >
> > <http://www.knifecenter.com/kc_new/store_detail.html?s=SOG31>
> > <http://www.knifecenter.com/kc_new/store_detail.html?s=SOG31>
> >
> > Now that's what I call a tool!
> >
> >
> >
> > -----Original Message-----
> > From: owner-vmd-l_at_ks.uiuc.edu
> > [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of John Stone
> > Sent: Friday, February 10, 2006 3:59 PM
> > To: L. Michel Espinoza-Fonseca
> > Cc: vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: VMD 1.8.4 beta 11 test
> > version available
> >
> >
> > Hi,
> > The Paratool extension/plugin is all-new and
> > the author,
> > Jan Saam, hasn't had time to write up
> > documentation just yet.
> > If you're interested in trying it out, you can
> > contact him:
> > http://bioinf.charite.de/biophys/people/saam/
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Sat, Feb 11, 2006 at 12:43:07AM +0100, L. Michel
> > Espinoza-Fonseca wrote:
> >
> >
> > HI all,
> >
> > Does anybody have a tutorial on how to
> > use the paratool plugin? I'm
> > really interested about it, but I
> > didn't find any specific
> >
> >
> > information
> >
> >
> > on how to use it.
> >
> > Thanks!
> > Cheers,
> > Michel
> >
> >
> > --
> > 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
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > --
> > ---------------------------
> > Jan Saam
> > Institute of Biochemistry
> > Charite Berlin
> > Monbijoustr. 2
> > 10117 Berlin
> > Germany
> >
> > +49 30 450-528-446
> > saam_at_charite.de
> > 

-- 
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