From FreeBio
Jeremy,
I apologize for taking so long to reply to your earlier inquiry.
As far as distribution of the group contribution code or executables goes,
my advisors decide on all such lab policies, and they are both currently out
of town on extended trips.
I can tell you about the program we use to determine the charge of the
predominant ion of a molecule at a specified pH. This program is a part of a
package called MarvinBeans which can be downloaded/licensed here:
http://www.chemaxon.com/marvin/
Now much of this package is free for use, no strings attached. However, I do
not know if the predominant ion calculator falls under that envelope. I find
the license agreement a bit on the vague side, so this is not immediately
clear to me.
Now I know Genomatica and the Palsson lab use a different package to
determine their charges, and I don't know what package they use.
I hope that clarifies things for you.
Chris
-----Original Message-----
From: Jeremy Zucker [mailto:zucker@research.dfci.harvard.edu]
Sent: Tuesday, June 20, 2006 4:07 PM
To: Christopher Henry
Cc: 'Adam Feist'; 'Markus Krummenacker'
Subject: Re: model comparison
Hi Adam or Chris,
Christopher Henry wrote:
Peter,
You do raise an important point regarding the molfiles that I sent out. The
majority of these molfiles come from the KEGG, although over 300 were hand
made or modified/corrected by me. Furthermore, all of these molfiles were
processed using a third party program to appropriately protonate the
compounds based on a pH of 7.
What is the name of the third party program to appropriately protonate
the compounds based on a pH of 7?
Sincerely,
Jeremy
