From owner-chemistry@ccl.net Thu Sep 12 16:32:00 2024
From: "Scott Brozell sbrozell||comcast.net" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: Announcement: Release of DOCK 6.12
Message-Id: <-55221-240912162304-24679-tgcPs67quQpsv+1k6xuA2w++server.ccl.net>
X-Original-From: Scott Brozell <sbrozell- -comcast.net>
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Date: Thu, 12 Sep 2024 16:22:27 -0400
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Sent to CCL by: Scott Brozell [sbrozell*_*comcast.net]

We are pleased to announce the release of DOCK 6.12.

DOCK is a suite of programs for molecular docking.  
The source code for DOCK 6.12 is available for download and free
for academic users at https://dock.compbio.ucsf.edu/DOCK_6/index.htm

This release includes several major new features:
A new implementation of the hierarchical database search method of
DOCK 3 which samples ligand degrees of freedom from precomputed
conformations, a new covalent docking algorithm called attach-and-grow
which aligns covalent residues and dummy atoms on ligands to grow
conformations, a new receptor desolvation scoring function based on
GIST, and updates to the chemgrid scoring function to match DOCK 3.7.

For full information on what is new in DOCK 6.12, please visit:

      https://dock.compbio.ucsf.edu/DOCK_6/new_in_6.12.txt

Sincerely,

The DOCK Team

Please visit us at the DOCK Web site.
https://dock.compbio.ucsf.edu


From owner-chemistry@ccl.net Thu Sep 12 23:28:01 2024
From: "michaelmorgan937 ~ gmail.com" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL: web application for orbital calculation and plot
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Sent to CCL by: [michaelmorgan937++gmail.com]
Thank you all for your kind help! All these apps are great and very helpful.

Michael

-----Original Message-----
> From: owner-chemistry+michaelmorgan937==gmail.com::ccl.net
<owner-chemistry+michaelmorgan937==gmail.com::ccl.net> On Behalf Of Jans
Alzate Morales jalzate+*+utalca.cl
Sent: Friday, September 6, 2024 4:13 PM
To: Morgan, Michael  <michaelmorgan937::gmail.com>
Subject: CCL: web application for orbital calculation and plot

Dear Michael,

I hope you're doing great.
You can try IQMol (http://www.iqmol.org/).
It allows you to draw the structure and submit the QM calculation at a
different level of theory using the server for a maximum of 10 minutes.
I have calculated QM energies for the imidazole ring to calculate the pKa
value using IQMol.

Best regards,

Jans

**********************************************

Jans Alzate-Morales, FRSC
Pharmaceutical Chemist, PhD. in Chemistry Associate Professor Centre for
Bioinformatics, Simulations and Modeling (CBSM) Universidad de Talca
1 Poniente 1141, Casilla 721, Talca - Chile
Teléfono: 56-71-201 798,
Email: jalzatemorales,gmail.com<mailto:jalzatemorales,gmail.com> or
jalzate,utalca.cl<mailto:jalzate,utalca.cl>
URL: http://cbsm.utalca.cl/?page_id=73   and http://doctorado.cbsm.cl

De: owner-chemistry+jalzate==utalca.cl,ccl.net
<owner-chemistry+jalzate==utalca.cl,ccl.net> en nombre de Michael Morgan
michaelmorgan937]-[gmail.com <owner-chemistry,ccl.net>
Fecha: viernes, 6 de septiembre de 2024 a las 16:50
Para: Jans Alzate Morales <jalzate,utalca.cl>
Asunto: CCL: web application for orbital calculation and plot

Sent to CCL by: "Michael  Morgan" [michaelmorgan937*gmail.com] Hi everyone,

Is there any web application I can use to draw a structure, request a
simple, on-the-fly qm calculation, and show a specific orbital from the
calculation result? It is for an undergraduate class, so the orbital plot
just need to be qualitatively correct. Semi-empirical calculations should do
the job.

Any suggestion? Thank you very much.
Michaelhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistr
y/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_CPWP152MB5467DD454CED
A1446583C21AB89E2CPWP152MB5467LAMP_
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<div class="WordSection1"> <p class="MsoNormal"><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US">Dear
Michael,<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span>
</p>
<p class="MsoNormal"><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US">I hope you're doing
great.<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US">You can try IQMol
(http://www.iqmol.org/).
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US">It allows you to draw
the structure and submit the QM calculation at a different level of theory
using the server for a maximum of 10 minutes.<o:p></o:p></span></p> <p
class="MsoNormal"><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US">I have calculated QM
energies for the imidazole ring to calculate the pKa value using
IQMol.<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span>
</p>
<p class="MsoNormal"><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US">Best
regards,<o:p></o:p></span></p> <p class="MsoNormal"><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span>
</p>
<p class="MsoNormal"><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US">Jans<o:p></o:p></span></
p>
<p class="MsoNormal"><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span>
</p>
<p class="MsoNormal"><span lang="EN-US"
style="font-size:12.0pt;color:black;mso-fareast-language:EN-US">************
**********************************<br>
<br>
Jans Alzate-Morales, FRSC<br>
Pharmaceutical Chemist, PhD. in&nbsp;Chemistry<br> Associate Professor<br>
Centre for Bioinformatics, Simulations&nbsp;and Modeling (CBSM)<br>
Universidad de Talca<br>
1 Poniente 1141, Casilla 721, Talca - Chile &nbsp;<br>
Teléfono: 56-71-201 798,&nbsp;<br>
Email:&nbsp;</span><span
style="font-size:12.0pt;mso-fareast-language:EN-US"><a
href="mailto:jalzatemorales,gmail.com"
title="mailto:jalzatemorales,gmail.com"><span lang="EN-US"
style="color:#0078D7">jalzatemorales,gmail.com</span></a></span><span
lang="EN-US"
style="font-size:12.0pt;color:black;mso-fareast-language:EN-US">&nbsp;or&nbs
p;</span><span style="font-size:12.0pt;mso-fareast-language:EN-US"><a
href="mailto:jalzate,utalca.cl" title="mailto:jalzate,utalca.cl"><span
lang="EN-US" style="color:#0078D7">jalzate,utalca.cl</span></a></span><span
lang="EN-US"
style="font-size:12.0pt;color:black;mso-fareast-language:EN-US">&nbsp;&nbsp;
<br>
URL:&nbsp;</span><span
style="font-size:12.0pt;mso-fareast-language:EN-US"><a
href="http://cbsm.utalca.cl/?page_id=73"
title="http://cbsm.utalca.cl/?page_id=73"><span lang="EN-US"
style="color:#0078D7">http://cbsm.utalca.cl/?page_id=73</span></a></span><sp
an lang="EN-US"
style="font-size:12.0pt;color:black;mso-fareast-language:EN-US">&nbsp;&nbsp;
&nbsp;and&nbsp;</span><span
style="font-size:12.0pt;mso-fareast-language:EN-US"><a
href="http://doctorado.cbsm.cl" title="http://doctorado.cbsm.cl"><span
lang="EN-US"
style="color:#0078D7">http://doctorado.cbsm.cl</span></a></span><span
lang="EN-US"
style="font-size:12.0pt;color:black;mso-fareast-language:EN-US">&nbsp;&nbsp;
</span><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"
style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p>&nbsp;</o:p></span>
</p>
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<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm
0cm"> <p class="MsoNormal" style="margin-bottom:12.0pt"><b><span
style="font-size:12.0pt;color:black">De:
</span></b><span
style="font-size:12.0pt;color:black">owner-chemistry+jalzate==utalca.cl,ccl.
net &lt;owner-chemistry+jalzate==utalca.cl,ccl.net&gt; en nombre de Michael
Morgan michaelmorgan937]-[gmail.com &lt;owner-chemistry,ccl.net&gt;<br>
<b>Fecha: </b>viernes, 6 de septiembre de 2024 a las 16:50<br>
<b>Para: </b>Jans Alzate Morales &lt;jalzate,utalca.cl&gt;<br>
<b>Asunto: </b>CCL: web application for orbital calculation and
plot<o:p></o:p></span></p> </div> <div> <p class="MsoNormal"
style="margin-bottom:12.0pt"><span style="font-size:11.0pt"><br> Sent to CCL
by: &quot;Michael&nbsp; Morgan&quot; [michaelmorgan937*gmail.com]<br> Hi
everyone,<br> <br> Is there any web application I can use to draw a
structure, request a simple, <br> on-the-fly qm calculation, and show a
specific orbital from the calculation <br> result? It is for an
undergraduate class, so the orbital plot just need to be <br> qualitatively
correct. Semi-empirical calculations should do the job. <br> <br> Any
suggestion? Thank you very much.<br> Michael<br> <br> <br> <br<br<br=r<br>
<br<br> &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <a
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