Subject: RE: CCL:Adding counterions on a protein

From: Robert Flight <l72k6..at..unb.ca>
Date: Thu, 24 Jul 2003 15:49:36 -0300

Hi Sandro,

I dont know about scripts, but I do know that GRID is supposedly capable of 
calculating interaction energies and finding energetically favorable sites for 
counterions in proteins.  I havent tried it myself, but I have seen it listed 
in the user manual.

http://www.moldiscovery.com/docs/grid21/index.html
http://www.moldiscovery.com/soft_grid.php

Cheers,

-Robert

>===== Original Message From sa.cosco..at..virgilio.it =====
>Dear All
>Does anybody know if there is an efficient script to add counterions on
>a protein in a random way?
>Actually, I tried to perform it with InsightII and Sybyl scripts but they
>have been constructed for nucleotides. Would it be possible to get scripts
>properly modified for proteins working with InsightII or Sybyl programs?
>Thanks in advance for your help.
>Best regards
>Sandro
>
>
>
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********************************
Robert Flight
Masters Student
Department of Chemistry
University of New Brunswick
Fredericton, NB  Canada  E3B 6E2
e-mail: robert.flight..at..unb.ca
 
********************************

"People think it must be fun to be a super genius, but they don't realize how hard it is to put up with all the idiots in the world."
-Calvin from Calvin & Hobbes

---

From: Ken Butenhof <kenb<<at>>accelrys.com>
Date: Thu, 24 Jul 2003 14:43:21 -0400

Hello Sandro,

There are many scripts in Accelrys' on-line BCL script library for use 
with Insight II.  One of these scripts is called counterion.bcl.  This 
script will place counterions suitable for use with several different 
force fields for charged residues in RNA/DNA or PEPTIDES.  The script uses 
a template recognition method to determine a suitable initial placement. 
Additional recognition templates can be added.  Be sure to read the 
scripts header information closely for any dependant scripts that will 
need to be downloaded with it.  The main script's name is counterion.bcl. 
The link is 
http://www.accelrys.com/support/life/scripts/bcl_lib.html

Best wishes,

Ken
_______________________________________________
Kenneth Butenhof          phone:  800 756-4674
Principal Scientist          email:    kenb<<at>>accelrys.com
Accelrys Inc.                   web:     www.accelrys.com

sa.cosco<<at>>virgilio.it 
Sent by: "Computational Chemistry List" <chemistry-request<<at>>ccl.net>
07/24/2003 12:56 PM

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Subject
CCL:Adding counterions on a protein

Dear All

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