Subject: CCL:assigning protonation states

From: Szabolcs Csepregi <szabolcs.csepregi<<at>>chemaxon.hu>
Date: Fri, 14 Jan 2005 14:35:06 +0100

Dear Luca,

Marvin has relevant calculator plugins for related tasks, namely
the "major microspecies" and "pKa" plugins.

"Major microspecies" is able to generate the highest concentration
protonation state at a given pH, and "pKa" can show the distributions of
each microspecies concentration along the whole pH range.

Marvin plugins are accessible from the Marvin GUIitself, but you can use 
them in JAVA programs using these classes:

http://www.chemaxon.com/marvin/doc/api/chemaxon/marvin/calculations/MajorMicrospeciesPlugin.html

http://www.chemaxon.com/marvin/doc/api/chemaxon/marvin/calculations/pKaPlugin.html

(there is some example code in the class headers)
Furthermore, we provide the command line tool cxcalc:

cxcalc majorms -H 3.2 test.mol
id      major-ms
1       [NH3+]C1C(Cl)OC(C(CCl)C1C([O-])=O)C([O-])=O

(You set the pH in -H)
In the following release there will be possible to set the major-ms
format other than SMILES (e.g. mol or sdf) but sorry, no mol2 support in
marvin. I suggest to use something like Open Babel for converting the
results.

For a list of command line parameters, type:

cxcalc majorms -h

And finally about the price tag: From your email address it seems that
you are in academia, so you can join the ChemAxon academic program and
use any of our software free of charge. For more information about this
and to download marvin, please visit www.chemaxon.com

Best regards,

Szabolcs
---
Szabolcs Csepregi, PhD
ChemAxon Ltd., Maramaros koz 3/A, Budapest, 1037 Hungary
http://www.chemaxon.com
Tel: +361 4532661