From owner-chemistry@ccl.net Fri Feb 15 00:37:00 2008
From: "Prashant Kumar prashantkbio#%#gmail.com" <owner-chemistry:_:server.ccl.net>
To: CCL
Subject: CCL: from SMILES/MDL to gif/png
Message-Id: <-36301-080215003539-15329-+pru4QUvyy939xBuOOOiAQ:_:server.ccl.net>
X-Original-From: "Prashant Kumar" <prashantkbio]^[gmail.com>
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Date: Fri, 15 Feb 2008 11:05:27 +0530
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Sent to CCL by: "Prashant Kumar" [prashantkbio#,#gmail.com]
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Dear Giulia,
                 try NCI browser .
n Thu, Feb 14, 2008 at 2:32 PM, Giulia Caron giulia.caron##unito.it <
owner-chemistry-*-ccl.net> wrote:

>
> Sent to CCL by: "Giulia  Caron" [giulia.caron . unito.it]
> Dear all,
>
> I am looking for a free generator (for Web-based applications) of 2D
> chemical structures in gif/png/... format from a SMILES/MDL input.
>
> Best regards
>
> Giulia>
>
>

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Dear Giulia, <br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; try NCI browser . <br><div class="gmail_quote">n Thu, Feb 14, 2008 at 2:32 PM, Giulia Caron giulia.caron##unito.it &lt;<a href="mailto:owner-chemistry-*-ccl.net">owner-chemistry-*-ccl.net</a>&gt; wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Sent to CCL by: &quot;Giulia &nbsp;Caron&quot; [giulia.caron . <a href="http://unito.it" target="_blank">unito.it</a>]<br>
Dear all,<br>
<br>
I am looking for a free generator (for Web-based applications) of 2D chemical structures in gif/png/... format from a SMILES/MDL input.<br>
<br>
Best regards<br>
<br>
Giulia<br>
<br>
<br>
<br<br<br<br<br>
<br>
E-mail to subscribers: <a href="mailto:CHEMISTRY-*-ccl.net">CHEMISTRY-*-ccl.net</a> or use:<br>
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From owner-chemistry@ccl.net Fri Feb 15 01:14:00 2008
From: "Aniko Simon aniko{=}simbiosys.ca" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL: vHTS: DOCK or AUTODOCK ?
Message-Id: <-36302-080215011134-32535-XnKohn8YlVvx9BI8GNcv6g[a]server.ccl.net>
X-Original-From: "Aniko  Simon" <aniko~!~simbiosys.ca>
Date: Fri, 15 Feb 2008 01:11:30 -0500


Sent to CCL by: "Aniko  Simon" [aniko/./simbiosys.ca]
Dear Jerome,

May I suggest trying eHiTS? eHiTS is free for academic research and has been shown to perform very well for virtual screening, for example in a recent evaluation from Merck:
http://www.simbiosys.ca/ehits/ehits_enrichment.html

Also, a very nice feature of eHiTS is the control over the Speed / Accuracy trade-off. By adjusting a simple parameter you can go from speeds of 15-20 seconds/ligand upto 20 minutes/ligand.  More info on speed is posted here:
http://www.simbiosys.ca/ehits/ehits_speed.html

We find that running in a relatively quick mode (40 - 60 sec / ligand) gives very good screening result. Then, you can easily move to a more accurate setting for the "hits" from the first screen for binding pose analysis.

If you want to try it out, just fill out a demo request:
http://www.simbiosys.ca/products/demo_request.html

Best regards,
Aniko

-- 
Aniko Simon, Ph.D.
SimBioSys Inc.
http://www.simbiosys.ca/
Tel: 1-416-741-4263

> Sent to CCL by: "Jerome  Baudry" [jerome=scs.uiuc.edu]
> Dear All
>
> I have been using commercial applications to perform virtual high
> throughput screening of virtual databases of compounds (a la ZINC) in
> protein models. I have access to a bunch of processors for embarrassingly
> parallel calculations, but the databases I want to screen are large.
>
> I would like to use free academic code, but it is not clear if DOCK (UCSF)
> or AUTODOCK (Scripps) will be able to process large databases of compounds
> - 700K cmpds or larger - in a reasonable time. I have seen results with
> AUTODOCK used to screen databases, but the published speed was about 1000
> molecules per week on 32 procs, which is way slower that with, say,
> LigandFit (30K cmpds / day on 16 procs in my experience). I have not seen
> benchmark for DOCK in vHTS mode.
>
> Now I understand that speed is not everything, and that quality of the
> binding pose is important, but I am looking at screening very large
> databases and I first want to do it in a reasonable time. I can eventually
> spend more time redocking the top of the large database in a 'slow but more
> accurate' mode.
>
> So my questions: do you know how DOCK & AUTODOCK handle vHTS of large
> databases? Any personal experience or additional papers? Any one of these
> two programs is better than the other for vHTS?
>
> Thanks a lot in advance,
>
> Jerome Baudry
> UT/ORNL Center for Molecular Biophysics, Oak Ridge National Lab, TN.
> jerome]_[scs.uiuc.edu


From owner-chemistry@ccl.net Fri Feb 15 03:23:00 2008
From: "Chupakhin Vladimir chupvl_._gmail.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: How to calculate number of rotatable bonds with ligand automatica
Message-Id: <-36303-080214045525-21878-GHa3AL4khZxupve5hNN5Dw,+,server.ccl.net>
X-Original-From: "Chupakhin Vladimir" <chupvl~!~gmail.com>
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Date: Thu, 14 Feb 2008 11:50:34 +0300
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Sent to CCL by: "Chupakhin Vladimir" [chupvl~!~gmail.com]

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Try Free and Open Chemoinformatics Software - CDK, Joelib2

http://almost.cubic.uni-koeln.de/cdk/cdk_top
http://www-ra.informatik.uni-tuebingen.de/software/joelib/

Vladimir Chupakhin


On Wed, Feb 13, 2008 at 11:20 PM, David Hose Anthrax_brothers~!~hotmail.com
<owner-chemistry#ccl.net> wrote:

>
> Sent to CCL by: "David  Hose" [Anthrax_brothers|,|hotmail.com]
> Many of the QSAR packages will do this.
>
> Dragon:
> http://www.talete.mi.it/help/dragon_help/index.html?IntroducingDRAGON
>
> For the Online version of Dragon: http://www.vcclab.org/lab/edragon/
>
> CODESSA: http://www.semichem.com/codessa/cfeatures.php
>
> Regards,
>
> Dave.
>
> -----
>
> Sent to CCL by: "Maxim Kholin" [maxim.kholin ~~ q-pharm.com]
> Dear Richie,
> Please try q-Mol, the free demo is downloadable from
> http://www.q-lead.com/qmol
> Maxim
>
>
>
>
> ----- Original Message -----
> > From: "Richie Wang f93548056:_:ntu.edu.tw" <owner-chemistry- -ccl.net>
> To: "Kholin, Maxim N " <maxim.kholin- -q-pharm.com>
> Sent: Wednesday, February 13, 2008 11:39 AM
> Subject: CCL: How to calculate number of rotatable bonds with ligand
> automatically?
>
>
> >
> > Sent to CCL by: "Richie Wang" [f93548056]_[ntu.edu.tw]
> > Dear all,
> >
> > Does somebody know what programs(free or not) could help to calculate
> > number of rotatable bonds with ligand automatically?
> >
> > Or, did any pulications or aligorithms ever mention about this?
> >
> > Best Regards,
> > Richie Wang>
>
>

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Try Free and Open Chemoinformatics Software - CDK, Joelib2<br><br><a href="http://almost.cubic.uni-koeln.de/cdk/cdk_top">http://almost.cubic.uni-koeln.de/cdk/cdk_top</a><br><a href="http://www-ra.informatik.uni-tuebingen.de/software/joelib/">http://www-ra.informatik.uni-tuebingen.de/software/joelib/</a><br>
<br>Vladimir Chupakhin<br><br><br><div class="gmail_quote">On Wed, Feb 13, 2008 at 11:20 PM, David Hose Anthrax_brothers~!~hotmail.com &lt;<a href="mailto:owner-chemistry#ccl.net">owner-chemistry#ccl.net</a>&gt; wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Sent to CCL by: &quot;David &nbsp;Hose&quot; [Anthrax_brothers|,|hotmail.com]<br>
Many of the QSAR packages will do this.<br>
<br>
Dragon: <a href="http://www.talete.mi.it/help/dragon_help/index.html?IntroducingDRAGON" target="_blank">http://www.talete.mi.it/help/dragon_help/index.html?IntroducingDRAGON</a><br>
<br>
For the Online version of Dragon: <a href="http://www.vcclab.org/lab/edragon/" target="_blank">http://www.vcclab.org/lab/edragon/</a><br>
<br>
CODESSA: <a href="http://www.semichem.com/codessa/cfeatures.php" target="_blank">http://www.semichem.com/codessa/cfeatures.php</a><br>
<br>
Regards,<br>
<br>
Dave.<br>
<br>
-----<br>
<br>
Sent to CCL by: &quot;Maxim Kholin&quot; [maxim.kholin ~~ <a href="http://q-pharm.com" target="_blank">q-pharm.com</a>]<br>
Dear Richie,<br>
Please try q-Mol, the free demo is downloadable from<br>
<a href="http://www.q-lead.com/qmol" target="_blank">http://www.q-lead.com/qmol</a><br>
Maxim<br>
<br>
<br>
<br>
<br>
----- Original Message -----<br>
&gt; From: &quot;Richie Wang f93548056:_:<a href="http://ntu.edu.tw" target="_blank">ntu.edu.tw</a>&quot; &lt;owner-chemistry- -<a href="http://ccl.net" target="_blank">ccl.net</a>&gt;<br>
To: &quot;Kholin, Maxim N &quot; &lt;maxim.kholin- -<a href="http://q-pharm.com" target="_blank">q-pharm.com</a>&gt;<br>
Sent: Wednesday, February 13, 2008 11:39 AM<br>
Subject: CCL: How to calculate number of rotatable bonds with ligand<br>
automatically?<br>
<br>
<br>
&gt;<br>
&gt; Sent to CCL by: &quot;Richie Wang&quot; [f93548056]_[<a href="http://ntu.edu.tw" target="_blank">ntu.edu.tw</a>]<br>
&gt; Dear all,<br>
&gt;<br>
&gt; Does somebody know what programs(free or not) could help to calculate<br>
&gt; number of rotatable bonds with ligand automatically?<br>
&gt;<br>
&gt; Or, did any pulications or aligorithms ever mention about this?<br>
&gt;<br>
&gt; Best Regards,<br>
&gt; Richie Wang&gt;<br>
&gt;<br>
<br>
<br>
<br<br<br<br<br>
<br>
E-mail to subscribers: <a href="mailto:CHEMISTRY#ccl.net">CHEMISTRY#ccl.net</a> or use:<br>
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<br>
</blockquote></div><br>

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From owner-chemistry@ccl.net Fri Feb 15 03:58:01 2008
From: "Lothar Terfloth lothar.terfloth ~~ mol-net.com" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL: from SMILES/MDL to gif/png
Message-Id: <-36304-080214123240-10195-6wa79u2VLcK9zYAqAAQsig#%#server.ccl.net>
X-Original-From: Lothar Terfloth <lothar.terfloth]~[mol-net.com>
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Date: Thu, 14 Feb 2008 17:42:00 +0100
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Sent to CCL by: Lothar Terfloth [lothar.terfloth .. mol-net.com]
Hello Guilia,

you may also take a look on our web service for this purpose at

http://www.molecular-networks.com/online_demons/image_demo.html

With best regards,

  Lothar

Giulia Caron giulia.caron##unito.it wrote:
> Sent to CCL by: "Giulia  Caron" [giulia.caron . unito.it]
> Dear all,
> 
> I am looking for a free generator (for Web-based applications) of 2D chemical structures in gif/png/... format from a SMILES/MDL input. 
> 
> Best regards
> 
> Giulia
-- 
--------------------------------------------------------
  Dr. Lothar Terfloth              Tel. +49-9131-9790623
  Molecular Networks GmbH          Fax: +49-9131-815 669

      Henkestr. 91
      D-91052 Erlangen
      Germany

      email:  Lothar.Terfloth:-:mol-net.com
      www:    http://www.mol-net.com
--------------------------------------------------------


From owner-chemistry@ccl.net Fri Feb 15 17:12:39 2008
From: "Aleksey Kuznetsov AlexKuznetsov2007[]yandex.ru" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL:G: Very strange HUGE binding energies for Pd atom and dimer on TiO2(110) surface
Message-Id: <-36306-080215162237-4107-Mzko45kY7zYPeskfe0v3vw[*]server.ccl.net>
X-Original-From: Aleksey Kuznetsov <AlexKuznetsov2007#%#yandex.ru>
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Date:   Fri, 15 Feb 2008 23:28:29 +0300
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Sent to CCL by: Aleksey Kuznetsov [AlexKuznetsov2007{=}yandex.ru]
Dear All,

I'd like to ask you for advice on this very strange issue: 
I do very simple GAUSSIAN calculations for Pd atom and dimer on TiO2(110) surface using the following conditions: B3LYP/LanL2mb level, Ti17O42H16 model, only Pd atoms in dimer were allowed to relax, for Pd atom I did single-point calculation, and I obtain HUGE binding energies for both cases - 3.2 eV for Pd atom and 6 eV for Pd dimer on surface. Comparing these with other theoretical studies I see that I get bonding energies overestimation by 2-3 times. Could anybody advise me on this issue? Can the BSSE play such a big role in this case? 

Thanks a lot,

With kind regards,
Aleksey Kuznetsov.
-------------------------------------------
Dr. Aleksey Kuznetsov
Cherry L. Emerson Center for Scientific Computation
Emory University
1515 Dickey Drive
Atlanta, GA 30322
USA

Phone: (404)727-2381
Email: akuznets%euch4e.chem.emory.edu
-------------------------------------------


From owner-chemistry@ccl.net Fri Feb 15 17:59:01 2008
From: "Jan Labanowski janl[-]speakeasy.net" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: CCL.NET Server has chest pains
Message-Id: <-36307-080215115005-4231-PfZ1xEZNe/RXbdly124K3w{:}server.ccl.net>
X-Original-From: Jan Labanowski <janl_+_speakeasy.net>
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Date: Fri, 15 Feb 2008 11:49:53 EST
MIME-Version: 1.0


Sent to CCL by: Jan Labanowski [janl[a]speakeasy.net]
Dear CCL,

CCL.NET server is having some problems (shows bad sectors on the hard
drive), or in plain English, it will die any moment...

I will be rebuilding it soon (of course, it always comes when I have
a few other high priority things to do...).

So expect the unexpected, like these winning Internet lottery tickets
that you get every day...

Thank you for your patience and your contributions.

Jan
CCL Monger


From owner-chemistry@ccl.net Fri Feb 15 20:15:00 2008
From: "Jeff Woodford jwoodfor[-]eou.edu" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian 03: custom density functionals
Message-Id: <-36308-080215163359-5163-yhdQNg4IxEhWVa6CEtgGMg{=}server.ccl.net>
X-Original-From: "Jeff Woodford" <jwoodfor^_^eou.edu>
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Sent to CCL by: "Jeff Woodford" [jwoodfor_+_eou.edu]
This is a multi-part message in MIME format.

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All:

Is it possible in Gaussian 03 to define a custom density functional, i.e.,
the KT3 exchange functional (J. Chem. Phys., 121, 5654, 2004)?

 

Thanks,

-Jeff

 

Jeffrey N. Woodford

Associate Professor of Chemistry

Eastern Oregon University

Tel: 541-962-3321

Fax: 541-962-3873

 


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<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>All:<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Is it possible in Gaussian 03 to define a custom =
density
functional, i.e., the KT3 exchange functional (J. Chem. Phys., 121, =
5654,
2004)?<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'><o:p>&nbsp;</o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>Thanks,<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
font-family:Arial'>-Jeff<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;
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From owner-chemistry@ccl.net Fri Feb 15 21:02:00 2008
From: "Wai-To Chan chan!^!curl.gkcl.yorku.ca" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL:G: Very strange HUGE binding energies for Pd atom and dimer on
Message-Id: <-36309-080215205906-5839-dXCND8SpYMbDF50o93RD2w|a|server.ccl.net>
X-Original-From: Wai-To Chan <chan ~~ curl.gkcl.yorku.ca>
Content-Transfer-Encoding: 7bit
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Date: Fri, 15 Feb 2008 21:04:39 -0500 (EST)
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Sent to CCL by: Wai-To Chan [chan(a)curl.gkcl.yorku.ca]
<<<<<<<<<<<<<<<<
 I'd like to ask you for advice on this very strange issue:
I do very simple GAUSSIAN calculations for Pd atom and dimer on TiO2(110)
surface using the following conditions: B3LYP/LanL2mb level, Ti17O42H16 model,
only Pd atoms in dimer were allowed to relax, for Pd atom I did single-point
calculation, and I obtain HUGE binding energies for both cases - 3.2 eV for Pd
atom and 6 eV for Pd dimer on surface. Comparing these with other theoretical
studies I see that I get bonding energies overestimation by 2-3 times. Could
anybody advise me on this issue? Can the BSSE play such a big role in this case?
 Thanks a lot,
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>


     Some years ago I did a bunch of DFT calculations on the complexation
between NH3 and a series of coinage metal clusters. I used mainly the 
SDD ECP but also experimented with all-electron basis sets. 

   With ECP effects of BSSE was pretty much negligible. Although I 
can't remember the rationale of it but I do remember my understanding
back then was that the small BSSE effect with ECP can be genealized
to other systems. 

	 One possible source of error could be the absence of polarization
functions on the O atoms. When using ECP like SDD and Lanl2dz
Gaussian by default assigns the D95 basis sets to the non-metal atoms.  
> From my experience using D95** instead of D95, that is augmentation 
of SDD and Lanl2dz with appropriate polarization functions on
the non-metal atoms, gives substantial improvement in 
the calculated energetics. 

   I am not familiar with the Lanl2mb basis you used so I don't 
know if it is amenable to similar basis set augmentation. I presume
the size of the surface you calculate could be too large for augmented
lanl2dz. In your situation a trick I may try is to assign polarization 
functions just to the atoms of the binding site. 


Wai-To Chan