VMD-L Mailing List

From: Jan Saam (saam_at_charite.de)
Date: Fri Feb 10 2006 - 18:29:34 CST

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>
>
>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