From owner-chemistry@ccl.net Mon Apr 26 12:43:00 2010
From: "Heath Watts hdw115(~)psu.edu" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL:G: TZV2D basis set
Message-Id: <-41713-100426115252-24904-plGl9kmxyaPcRch4LsPMVg^^server.ccl.net>
X-Original-From: Heath Watts <hdw115,,psu.edu>
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Date: Mon, 26 Apr 2010 10:44:57 -0400
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Sent to CCL by: Heath Watts [hdw115!=!psu.edu]
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Hi,
I am looking for the TZV2D basis set, in Gaussian format for C, H, O, and N.
I've looked on EMSL, Turbomole, and Dr. Alrich's site, but haven't been able
to find the gbs file. I'd appreciate any assistance in finding this file
that you can provide.
Thanks,
Heath

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Hi,<br>I am looking for the TZV2D basis set, in Gaussian format for C, H, O=
, and N. I&#39;ve looked on EMSL, Turbomole, and Dr. Alrich&#39;s site, but=
 haven&#39;t been able to find the gbs file. I&#39;d appreciate any assista=
nce in finding this file that you can provide.<br>
Thanks,<br>Heath<br>

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From owner-chemistry@ccl.net Mon Apr 26 13:17:00 2010
From: "Kshatresh Dutta Dubey kshatresh : gmail.com" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL: query about QMMM interaction energy
Message-Id: <-41714-100426111312-18278-hCEkx9UeJ+2uGKpOf6NoUA-$-server.ccl.net>
X-Original-From: Kshatresh Dutta Dubey <kshatresh[*]gmail.com>
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Date: Mon, 26 Apr 2010 20:43:05 +0530
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Sent to CCL by: Kshatresh Dutta Dubey [kshatresh()gmail.com]
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Dear All,
I am simulating a protein ligand complex using hybrid QM/MM methods. I want
to calculate QM- Interaction energy between QM region and MM region. The
output of program gives QMMM electrostatic energy, QMMM bond energy,QMMM
bend energy and QMMM torsion energy. Can i use

QM interaction energy = QMMM electrostatic+ QMMM bond +QMMM bend + QMMM
torsion

to calculate interaction between QM region and MM region or only QMMM
electrostatic energy? If no, then kindly suggest me to calculate such
interaction energy

Every help is heartily appreciated. Kindly give me some references related
with this methodology.

Thanks in advance.

Regards

Kshatresh Dutta Dubey
Biophysics Unit DDU Gorakhpur University

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<div class=3D"gmail_quote"><br><br>Dear All, <br>I am simulating a protein =
ligand complex using hybrid QM/MM methods. I want to calculate QM- Interact=
ion energy between QM region and MM region. The output of program gives QMM=
M electrostatic energy, QMMM bond energy,QMMM bend energy and QMMM torsion =
energy. Can i use <br>

<br>QM interaction energy =3D QMMM electrostatic+ QMMM bond +QMMM bend + QM=
MM torsion<br><br>to calculate interaction between QM region and MM region =
or only QMMM electrostatic energy? If no, then kindly suggest me to calcula=
te such interaction energy<br>

<br>Every help is heartily appreciated. Kindly give me some references rela=
ted with this methodology. <br><br>Thanks in advance.<br><br>Regards<br><fo=
nt color=3D"#888888"><br>Kshatresh Dutta Dubey<br>Biophysics Unit DDU Gorak=
hpur University<br>
<br><br><br>
</font></div><br>

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From owner-chemistry@ccl.net Mon Apr 26 13:52:00 2010
From: "Heath Watts hdw115[A]psu.edu" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL:G: TZV2D basis set
Message-Id: <-41715-100426134944-17950-o6QdU0kPSCDdHYuddmRVVA(a)server.ccl.net>
X-Original-From: Heath Watts <hdw115(_)psu.edu>
Content-Type: multipart/alternative; boundary=000e0cd1750e5eb24e04852766be
Date: Mon, 26 Apr 2010 13:49:34 -0400
MIME-Version: 1.0


Sent to CCL by: Heath Watts [hdw115|,|psu.edu]
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Please pardon my misspelling, I meant Dr. Ahlrichs.
Heath

On Mon, Apr 26, 2010 at 10:44 AM, Heath Watts hdw115(~)psu.edu <
owner-chemistry%%ccl.net> wrote:

> Hi,
> I am looking for the TZV2D basis set, in Gaussian format for C, H, O, and
> N. I've looked on EMSL, Turbomole, and Dr. Alrich's site, but haven't been
> able to find the gbs file. I'd appreciate any assistance in finding this
> file that you can provide.
> Thanks,
> Heath
>

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Please pardon my misspelling, I meant Dr. Ahlrichs.<br>Heath<br><br><div cl=
ass=3D"gmail_quote">On Mon, Apr 26, 2010 at 10:44 AM, Heath Watts hdw115(~)=
<a href=3D"http://psu.edu">psu.edu</a> <span dir=3D"ltr">&lt;<a href=3D"mai=
lto:owner-chemistry%%ccl.net">owner-chemistry%%ccl.net</a>&gt;</span> wrote:<=
br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Hi,<br>I am looki=
ng for the TZV2D basis set, in Gaussian format for C, H, O, and N. I&#39;ve=
 looked on EMSL, Turbomole, and Dr. Alrich&#39;s site, but haven&#39;t been=
 able to find the gbs file. I&#39;d appreciate any assistance in finding th=
is file that you can provide.<br>

Thanks,<br><font color=3D"#888888">Heath<br>
</font></blockquote></div><br>

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From owner-chemistry@ccl.net Mon Apr 26 20:36:00 2010
From: "case case:+:biomaps.rutgers.edu" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: Announcement: release of Amber11 and AmberTools 1.4
Message-Id: <-41716-100426094530-30731-K8wgSODFPx0usDUPH/zwoQ,,server.ccl.net>
X-Original-From: case <case%biomaps.rutgers.edu>
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Content-Type: text/plain; charset=us-ascii
Date: Mon, 26 Apr 2010 08:41:28 -0400
Mime-Version: 1.0


Sent to CCL by: case [case]_[biomaps.rutgers.edu]

I am pleased to announce the release Amber 11.

Amber is a suite of programs designed for molecular dynamics simulations of
biomolecules.  For full information on what is new in Amber 11, and how to
order it, please visit:

      http://ambermd.org/#Amber

I am also pleased are proud to announce the release of version 1.4 of 
AmberTools.

AmberTools consists of several independently developed packages that
work well by themselves, and with Amber itself. Key facilities allow the
preparation of systems for MD simulations, and analysis of trajectories.
The suite can also be used to carry out complete molecular mechanics
investigations (using NAB), employing generalized Born, Poisson-Boltzmann
or 3D-RISM solvent models.  AmberTools is released mainly using the GNU
General Public License (GPL), with some components using other open source
licenses.

For more information, and to download AmberTools, please visit:

      http://ambermd.org/#AmberTools

...dave case
(For the Amber development team: http://ambermd.org/contributors.html  )


From owner-chemistry@ccl.net Mon Apr 26 21:11:00 2010
From: "Isaac B Bersuker bersuker**cm.utexas.edu" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL: query about QMMM interaction energy
Message-Id: <-41717-100426151356-28937-kEKcGUzu402Gqrw1BGsY8A+/-server.ccl.net>
X-Original-From: Isaac B Bersuker <bersuker#cm.utexas.edu>
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Sent to CCL by: Isaac B Bersuker [bersuker()cm.utexas.edu]
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Dear Kshatresh Dutta Dubey, 



The separation of the total energy of the system in QM and MM parts plus the interaction between them is legitimate ONLY if the latter is small as compared with the former and can be considered as a small perturbation to the zero-order energies of the former (see I. B. Bersuker, In Computational Chemistry: Reviews of Current Trends , v. 6, Ed. J. Leszczynski, World Scientific, 2001, pp 69-135. 



Regards 

I. B. 

Dr. Isaac B. Bersuker 
Institute for Theoretical Chemistry 
The University of Texas at Austin 
Chem & Biochem Department 
1 University Station A5300 
Austin, TX 78712-0165 
Phone: (512) 471-4671; Fax: (512) 471-8696 
E-mail: bersuker##cm.utexas.edu 
http://www.cm.utexas.edu/isaac_bersuker 

----- Original Message ----- 
> From: "Kshatresh Dutta Dubey kshatresh : gmail.com" <owner-chemistry##ccl.net> 
To: "Isaac B.  Bersuker" <bersuker##mail.cm.utexas.edu> 
Sent: Monday, April 26, 2010 10:13:05 AM GMT -06:00 US/Canada Central 
Subject: CCL: query about QMMM interaction energy 




Dear All, 
I am simulating a protein ligand complex using hybrid QM/MM methods. I want to calculate QM- Interaction energy between QM region and MM region. The output of program gives QMMM electrostatic energy, QMMM bond energy,QMMM bend energy and QMMM torsion energy. Can i use 

QM interaction energy = QMMM electrostatic+ QMMM bond +QMMM bend + QMMM torsion 

to calculate interaction between QM region and MM region or only QMMM electrostatic energy? If no, then kindly suggest me to calculate such interaction energy 

Every help is heartily appreciated. Kindly give me some references related with this methodology. 

Thanks in advance. 

Regards 

Kshatresh Dutta Dubey 
Biophysics Unit DDU Gorakhpur University 





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<html><head><style type='text/css'>p { margin: 0; }</style></head><body><div style='font-family: Arial; font-size: 18pt; color: #000000'><P><FONT size=4>Dear <FONT color=#888888>Kshatresh Dutta Dubey,</FONT></FONT></P>
<P><FONT size=4><FONT color=#888888></FONT></FONT>&nbsp;</P>
<P><FONT size=4><FONT color=#888888>The separation of the total energy of the system in QM and MM parts plus the interaction between them is legitimate ONLY if the latter is small as compared with the former and can be considered as a small perturbation to the zero-order energies of the former (see I. B. Bersuker, In <EM>Computational Chemistry: Reviews of Current Trends</EM>, v. 6, Ed. J. Leszczynski, World Scientific, 2001, pp 69-135.</FONT></FONT></P>
<P><FONT size=4><FONT color=#888888></FONT></FONT>&nbsp;</P>
<P><FONT size=4><FONT color=#888888>Regards</FONT></FONT></P>
<P><FONT size=4><FONT color=#888888>I. B.</FONT><BR><BR>Dr. Isaac B. Bersuker<BR>Institute for Theoretical Chemistry<BR>The University of Texas at Austin<BR>Chem &amp; Biochem Department<BR>1 University Station A5300<BR>Austin, TX 78712-0165<BR>Phone: (512) 471-4671; Fax: (512) 471-8696<BR>E-mail: bersuker##cm.utexas.edu<BR>http://www.cm.utexas.edu/isaac_bersuker<BR><BR>----- Original Message -----<BR>From: "Kshatresh Dutta Dubey kshatresh : gmail.com" &lt;owner-chemistry##ccl.net&gt;<BR>To: "Isaac B.  Bersuker" &lt;bersuker##mail.cm.utexas.edu&gt;<BR>Sent: Monday, April 26, 2010 10:13:05 AM GMT -06:00 US/Canada Central<BR>Subject: CCL: query about QMMM interaction energy<BR><BR></P></FONT>
<DIV class=gmail_quote><BR><BR><FONT size=4>Dear All, <BR>I am simulating a protein ligand complex using hybrid QM/MM methods. I want to calculate QM- Interaction energy between QM region and MM region. The output of program gives QMMM electrostatic energy, QMMM bond energy,QMMM bend energy and QMMM torsion energy. Can i use <BR><BR>QM interaction energy = QMMM electrostatic+ QMMM bond +QMMM bend + QMMM torsion<BR><BR>to calculate interaction between QM region and MM region or only QMMM electrostatic energy? If no, then kindly suggest me to calculate such interaction energy<BR><BR>Every help is heartily appreciated. Kindly give me some references related with this methodology. <BR><BR>Thanks in advance.<BR><BR>Regards<BR></FONT><FONT color=#888888><BR>Kshatresh Dutta Dubey<BR>Biophysics Unit DDU Gorakhpur University<BR><BR><BR><BR></FONT></DIV><BR></div></body></html>
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