VMD-L Mailing List

From: Warren DeLano (warren_at_delsci.com)
Date: Fri Feb 10 2006 - 19:12:14 CST

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
>