From owner-chemistry@ccl.net Wed Mar 18 11:23:01 2009
From: "Zsolt Zsoldos zsolt]_[simbiosys.ca" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: Protonation states
Message-Id: <-38878-090318110541-22852-tVGtrsVZdj8ck9dqQyAysA*server.ccl.net>
X-Original-From: Zsolt Zsoldos <zsolt|-|simbiosys.ca>
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Date: Wed, 18 Mar 2009 10:32:23 -0400
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Sent to CCL by: Zsolt Zsoldos [zsolt[#]simbiosys.ca]
Hi Sergio,

As others have suggested, there are general force field techniques and
you can also use pKa estimation based methods if you are interested in
the most likely protonation state of the ligand in solution at a given
pH. However, you should be aware that if you want to use your ligand
for docking to a protein site, then computing the correct protonation
state is a much more complex task, and in fact it depends on the
specific pose of the ligand in the binding site. I have written a
detailed blog post about this question in response to an earlier (last
year) CCL posting, see here:
http://www.simbiosys.ca/blog/2008/05/17/correct-protonation-state-for-docking/

I hope this helps,
Zsolt

On Tue, Mar 17, 2009 at 3:57 PM, Sergio Mares-Samano
sergio.mares-samano,postgrad.manchester.ac.uk
<owner-chemistry-*-ccl.net> wrote:
>
> Sent to CCL by: Sergio Mares-Samano
> [sergio.mares-samano/a\postgrad.manchester.ac.uk]
> Hi,
>
> Which software (free/open source) can I use to assign the correct ligand
> protonation forms? I have a database of around 5000 molecules (smile format)
> and used open babel to convert them into the SDF's. After performing a
> google search, I found that OpenBabel was a good option to get the SDF's
> from the smiles. Now however, I'm struggling to find a program to assign the
> correct charges according to a certain pH e.g. 7.
>
> Any suggestions?
>
> Thank you very much in advance,
>
> Sergio Mares-Samanohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences:
> http://server.ccl.net/chemistry/announcements/conferences/>
>
>



-- 
Zsolt Zsoldos, PhD


From owner-chemistry@ccl.net Wed Mar 18 23:40:01 2009
From: "Muhammad Ramzan Saeed Janjua dr_janjua2010#,#yahoo.com" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL: Open Shell/ Close Shell
Message-Id: <-38879-090318213302-11699-ni9WRYepUmChYWfkLaqFHw : server.ccl.net>
X-Original-From: "Muhammad Ramzan Saeed Janjua" <dr_janjua2010/./yahoo.com>
Date: Wed, 18 Mar 2009 21:32:57 -0400


Sent to CCL by: "Muhammad Ramzan Saeed Janjua" [dr_janjua2010::yahoo.com]
Dear Colleagues,
Is there any rule or formula to find whether a particular molecule belongs to open shell or close shell?
Is there any corelation between spin plarization and spin multiplicity?

Thanks in anticipation!

Stay Bless,
Janjua
PhD Scholar at NENU P.R. China