From owner-chemistry@ccl.net Tue Aug 11 02:53:00 2009
From: "Karol M. Langner karol.langner .. gmail.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL:G: Counterpoise method
Message-Id: <-39965-090811025209-13583-uF/iNo5GcWLCce+QB+dQNQ,+,server.ccl.net>
X-Original-From: "Karol M. Langner" <karol.langner%%gmail.com>
Date: Tue, 11 Aug 2009 02:52:05 -0400


Sent to CCL by: "Karol M. Langner" [karol.langner . gmail.com]
Alessandra,

 If what you are looking for is the CP-corrected interaction energy, then I think you need to calculate:
CP-correct total energy - (Ea*+Eb*)
as per your nomenclature.

 You really should read through a few papers on the subject. A good place to start is Chem. Rev. 2000, 100, pp.42274252 and the references there in section IID.

Cheers,
Karol

> "Alessandra Mattei ale.mattei^uky.edu"  wrote:
> 
> Sent to CCL by: "Alessandra  Mattei" [ale.mattei.]=[.uky.edu]
> Dear CCL subscribers,
> 
> I am using Counterpoise method in G03 to calculate the energy of intermolecular interaction between two molecules (A and B). The output file gives 5 energy terms: dimer (Eab), monomers with ghost functions (Ea* and Eb*), monomers without ghost functions(Ea and Eb) energies. At the end of the file there are the CP corrected energy and BSSE for the interaction energy. Based on these values, what is the formula to calculate the intermolecular energy?
> Thanks for your help.
> 
> Alessandra Mattei
> University of Kentucky
> Department of Pharmaceutical Sciences
> 725 Rose St.
> Lexington, KY 40536


From owner-chemistry@ccl.net Tue Aug 11 05:17:01 2009
From: "Karol M. Langner karol.langner[a]gmail.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL:G: Counterpoise method
Message-Id: <-39966-090811051549-22970-WPWx1/ehrTD+y4VPnCLilQ++server.ccl.net>
X-Original-From: "Karol M. Langner" <karol.langner]_[gmail.com>
Date: Tue, 11 Aug 2009 05:15:45 -0400


Sent to CCL by: "Karol M. Langner" [karol.langner[#]gmail.com]
Sorry, what I wrote below is wrong. To get the corrected intermolecular interaction energy you need to subtract Ea* and Eb* from the non-corrected energy of the dimer (calculated and printed at the beginning).

The CP-corrected interaction energy that G03 prints is the energy of the dimer minus the BSSE energy. If you subtract Ea and Eb (monomers in their own basis sets) from this, you should get the same number as above.

Cheers,
Karol

> "Karol M. Langner karol.langner .. gmail.com"  wrote:
> 
> Sent to CCL by: "Karol M. Langner" [karol.langner . gmail.com]
> Alessandra,
> 
>  If what you are looking for is the CP-corrected interaction energy, then I think you need to calculate:
> CP-correct total energy - (Ea*+Eb*)
> as per your nomenclature.
> 
>  You really should read through a few papers on the subject. A good place to start is Chem. Rev. 2000, 100, pp.42274252 and the references there in section IID.
> 
> Cheers,
> Karol
> 
> > "Alessandra Mattei ale.mattei^uky.edu"  wrote:
> > 
> > Sent to CCL by: "Alessandra  Mattei" [ale.mattei.]=[.uky.edu]
> > Dear CCL subscribers,
> > 
> > I am using Counterpoise method in G03 to calculate the energy of intermolecular interaction between two molecules (A and B). The output file gives 5 energy terms: dimer (Eab), monomers with ghost functions (Ea* and Eb*), monomers without ghost functions(Ea and Eb) energies. At the end of the file there are the CP corrected energy and BSSE for the interaction energy. Based on these values, what is the formula to calculate the intermolecular energy?
> > Thanks for your help.
> > 
> > Alessandra Mattei
> > University of Kentucky
> > Department of Pharmaceutical Sciences
> > 725 Rose St.
> > Lexington, KY 40536
> 
>


From owner-chemistry@ccl.net Tue Aug 11 08:44:00 2009
From: "S Bill S_Bill36*_*yahoo.co.uk" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: reparamaterize semi-empirical PM3 parameters
Message-Id: <-39967-090811084329-8391-mRUrwddZPKD1zs/G7shebA- -server.ccl.net>
X-Original-From: "S  Bill" <S_Bill36() yahoo.co.uk>
Date: Tue, 11 Aug 2009 08:43:25 -0400


Sent to CCL by: "S  Bill" [S_Bill36[]yahoo.co.uk]
Dear CCL
I would appraciate any references/comments/recommadtions about how to learn to reparamaterize semi-empirical PM3 parameters for any ion (for example,Ca2+). In addition to any software free or cheap for this process.
Thanks in advance.
S. Bill


From owner-chemistry@ccl.net Tue Aug 11 09:19:00 2009
From: "Barbara Jagoda-Cwiklik barbara(~)fh.huji.ac.il" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL:G: Counterpoise method
Message-Id: <-39968-090811085121-11735-fu8uzdnEUmb8r6VkqsXZhw],[server.ccl.net>
X-Original-From: Barbara Jagoda-Cwiklik <barbara+/-fh.huji.ac.il>
Content-Type: multipart/alternative; boundary=0016363b96d47fc7ac0470dd274d
Date: Tue, 11 Aug 2009 15:50:59 +0300
MIME-Version: 1.0


Sent to CCL by: Barbara Jagoda-Cwiklik [barbara]~[fh.huji.ac.il]
--0016363b96d47fc7ac0470dd274d
Content-Type: text/plain; charset=ISO-8859-1
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On Tue, Aug 11, 2009 at 12:50 AM, Alessandra Mattei ale.mattei^uky.edu <
owner-chemistry{=}ccl.net> wrote:

>
> Sent to CCL by: "Alessandra  Mattei" [ale.mattei.{=}.uky.edu]
> Dear CCL subscribers,
>
> I am using Counterpoise method in G03 to calculate the energy of
> intermolecular interaction between two molecules (A and B). The output file
> gives 5 energy terms: dimer (Eab), monomers with ghost functions (Ea* and
> Eb*), monomers without ghost functions(Ea and Eb) energies. At the end of
> the file there are the CP corrected energy and BSSE for the interaction
> energy. Based on these values, what is the formula to calculate the
> intermolecular energy?
> Thanks for your help.
>
> Alessandra Mattei
> University of Kentucky
> Department of Pharmaceutical Sciences
> 725 Rose St.
> Lexington, KY 40536
>

Hi Alessandra,

It was already here (with a bit different notation):
http://www.ccl.net/chemistry/resources/messages/2007/01/02.001-dir/index.html
but again :-)

According to D.C.Young "Computational Chemistry":
E_interaction = E_AB,bAB - E_A,bAB - E_B,bAB        [formula 1]
where:
E_AB,bAB - E of AB complex in AB basis set
E_A,bAB  - E of monomer A in AB basis set
E_B,bAB  - E of monomer B in AB basis set

As you wrote, Gaussian in Counterpoise output presents the energies in the
following order:  E_AB,bAB,  E_A,bAB,  E_B,bAB and
E_A  - E of monomer A in A basis set
E_B  - E of monomer B in B basis set and in the end:
corrected energy (E_corrected) & BSSE energy.
Using above output you can also calculate interaction energy this way:
E_interaction = E_corrected - (E_A + E_B)                [formula 2]

Formulas 1 and 2 give the same result :)

Best,
Basia

Barbara Jagoda-Cwiklik, Ph.D
The Fritz Haber Research Center for Molecular Dynamics
Institute of Chemistry
The Hebrew University of Jerusalem
Jerusalem, ISRAEL
e-mail: barbara{=}fh.huji.ac.il

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<div dir=3D"ltr"><div class=3D"gmail_quote">On Tue, Aug 11, 2009 at 12:50 A=
M, Alessandra Mattei ale.mattei^<a href=3D"http://uky.edu">uky.edu</a> <spa=
n dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry{=}ccl.net">owner-chemistr=
y{=}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;"><br>
Sent to CCL by: &quot;Alessandra =A0Mattei&quot; [ale.mattei.{=}.<a href=3D"h=
ttp://uky.edu" target=3D"_blank">uky.edu</a>]<br>
Dear CCL subscribers,<br>
<br>
I am using Counterpoise method in G03 to calculate the energy of intermolec=
ular interaction between two molecules (A and B). The output file gives 5 e=
nergy terms: dimer (Eab), monomers with ghost functions (Ea* and Eb*), mono=
mers without ghost functions(Ea and Eb) energies. At the end of the file th=
ere are the CP corrected energy and BSSE for the interaction energy. Based =
on these values, what is the formula to calculate the intermolecular energy=
?<br>

Thanks for your help.<br>
<br>
Alessandra Mattei<br>
University of Kentucky<br>
Department of Pharmaceutical Sciences<br>
725 Rose St.<br>
Lexington, KY 40536<br>
</blockquote><div><br><pre style=3D"font-family: arial,helvetica,sans-serif=
;"><font size=3D"2">Hi Alessandra,<br><br>It was already here (with a bit d=
ifferent notation):<br><a href=3D"http://www.ccl.net/chemistry/resources/me=
ssages/2007/01/02.001-dir/index.html">http://www.ccl.net/chemistry/resource=
s/messages/2007/01/02.001-dir/index.html</a><br>
but again :-)<br><br>According to D.C.Young &quot;Computational Chemistry&q=
uot;:<br>E_interaction =3D E_AB,bAB - E_A,bAB - E_B,bAB        [formula 1]<=
br>where:<br>E_AB,bAB - E of AB complex in AB basis set<br>E_A,bAB  - E of =
monomer A in AB basis set<br>
E_B,bAB  - E of monomer B in AB basis set<br><br>As you wrote, Gaussian in =
Counterpoise output presents the energies in the<br>following order:  E_AB,=
bAB,  E_A,bAB,  E_B,bAB and<br>E_A  - E of monomer A in A basis set<br>
E_B  - E of monomer B in B basis set and in the end:<br>corrected energy (E=
_corrected) &amp; BSSE energy.<br>Using above output you can also calculate=
 interaction energy this way:<br>E_interaction =3D E_corrected - (E_A + E_B=
)                [formula 2]<br>
<br>Formulas 1 and 2 give the same result :)<br><br>Best,<br>Basia</font><f=
ont style=3D"font-family: arial,helvetica,sans-serif;" size=3D"2"> <br><br>=
</font>Barbara Jagoda-Cwiklik, Ph.D<br>The Fritz Haber Research Center for =
Molecular Dynamics<br>
Institute of Chemistry<br>The Hebrew University of Jerusalem<br>Jerusalem, =
ISRAEL<br>e-mail: <a href=3D"mailto:barbara{=}fh.huji.ac.il" target=3D"_blank=
">barbara{=}fh.huji.ac.il</a><br></pre></div></div>
</div>

--0016363b96d47fc7ac0470dd274d--


From owner-chemistry@ccl.net Tue Aug 11 09:59:01 2009
From: "Igor Avilov igor.avilov||fundp.ac.be" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL:G: error message Transition metal Porphyrin complex
Message-Id: <-39969-090811045541-20002-luvy3thlPTXSyLK5jlw0Kg(!)server.ccl.net>
X-Original-From: Igor Avilov <igor.avilov[a]fundp.ac.be>
Content-Transfer-Encoding: 8bit
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Date: Tue, 11 Aug 2009 10:03:13 +0200
MIME-Version: 1.0


Sent to CCL by: Igor Avilov [igor.avilov,+,fundp.ac.be]
Hi Morad,

It's strange that the calculation stopped without any error message. 
Sometimes the program crashes when you allocate more memory that it's 
available. Just for your information - it's not necessary to allocate 
that much memory for geometry optimization. I'd say 2GB would be more 
than enough.

Cheers,
Igor.

Morad M El-Hendawy M80elhendawy(a)yahoo.com wrote:
> Sent to CCL by: "Morad M El-Hendawy" [M80elhendawy:yahoo.com]
> Hi every body,
> I have a problem regarding the geometry optimization of transition metal porphyrin complex using Gaussian 9. Here the head and tail of output are:
>
> The head:
>  %chk=Co-Porph.chk
>  %mem=6GB
>  %nproc=8
>  Will use up to    8 processors via shared memory.
>  -----------------------------------------------
>  # opt=TIGHT b3lyp/6-311g(d,p) geom=connectivity
>  -----------------------------------------------
>
> The tail:
> Harris functional with IExCor=  402 diagonalized for initial guess.
>  ExpMin= 1.03D-01 ExpMax= 6.29D+03 ExpMxC= 9.49D+02 IAcc=1 IRadAn=         1 AccDes= 0.00D+00
>  HarFok:  IExCor=  402 AccDes= 0.00D+00 IRadAn=         1 IDoV= 1
>  ScaDFX=  1.000000  1.000000  1.000000  1.000000
>  FoFCou: FMM=F IPFlag=           0 FMFlag=      100000 FMFlg1=        2001
>          NFxFlg=           0 DoJE=T BraDBF=F KetDBF=T FulRan=T
>          Omega=  0.000000  0.000000  1.000000  0.000000  0.000000 ICntrl=     500 IOpCl=  0
>          NMat0=    1 NMatS0=    1 NMatT0=    0 NMatD0=    1 NMtDS0=    0 NMtDT0=    0
>          I1Cent=           4 NGrid=           0.
>  Petite list used in FoFCou.
>  Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
>  Requested convergence on MAX density matrix=1.00D-06.
>  Requested convergence on             energy=1.00D-06.
>  No special actions if energy rises.
>  Integral accuracy reduced to 1.0D-05 until final iterations.
>  Initial convergence to 1.0D-05 achieved.  Increase integral accuracy.
>
>
> Now, why the program stopped here and what is the suggested solution? I will be apperciated for your help
> kind regards,
> Morad El-Hendawy
> UCD,
> Ireland>
>
>   

-- 

------------------------------------------------
Igor Avilov

Université de Namur (FuNDP)
Centre de Recherche en Physique de la Matière et du Rayonnement (PMR)
Laboratoire LISE
61, Rue de Bruxelles
B-5000 Namur (Belgium)

Tél: +32 81 72 52 32  
Fax: +32 81 72 45 95
E-mail: igor.avilov|fundp.ac.be
web:http://www.fundp.ac.be/en/sci/physics/lise/
------------------------------------------------

***********************************
Visit our EU projects' websites:

http://www.icontrol-strep.eu/
http://www.nano2hybrids.net/
***********************************


From owner-chemistry@ccl.net Tue Aug 11 10:29:01 2009
From: "Thomas Patko tpatko _ gmail.com" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: reparamaterize semi-empirical PM3 parameters
Message-Id: <-39970-090811095041-19778-em5pTxP4vAx7vF19ejgd+A:-:server.ccl.net>
X-Original-From: Thomas Patko <tpatko[a]gmail.com>
Content-Type: multipart/alternative; boundary=0016e6471b94cb72770470dd59d7
Date: Tue, 11 Aug 2009 06:05:03 -0700
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Sent to CCL by: Thomas Patko [tpatko%%gmail.com]
--0016e6471b94cb72770470dd59d7
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Have you already tried PM6 for your system?  I should work out of the box
for nearly all atoms.

http://openmopac.net/MOPAC2009.html

Cheers,

Thomas

On Tue, Aug 11, 2009 at 5:43 AM, S Bill S_Bill36*_*yahoo.co.uk <
owner-chemistry::ccl.net> wrote:

>
> Sent to CCL by: "S  Bill" [S_Bill36[]yahoo.co.uk]
> Dear CCL
> I would appraciate any references/comments/recommadtions about how to learn
> to reparamaterize semi-empirical PM3 parameters for any ion (for
> example,Ca2+). In addition to any software free or cheap for this process.
> Thanks in advance.
> S. Bill>
>
>

--0016e6471b94cb72770470dd59d7
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Have you already tried PM6 for your system?=A0 I should work out of the box=
 for nearly all atoms.<br><br><a href=3D"http://openmopac.net/MOPAC2009.htm=
l">http://openmopac.net/MOPAC2009.html</a><br><br>Cheers,<br><br>Thomas<br>=
<br>
<div class=3D"gmail_quote">On Tue, Aug 11, 2009 at 5:43 AM, S Bill S_Bill36=
*_*<a href=3D"http://yahoo.co.uk">yahoo.co.uk</a> <span dir=3D"ltr">&lt;<a =
href=3D"mailto:owner-chemistry::ccl.net">owner-chemistry::ccl.net</a>&gt;</sp=
an> 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;"><br>
Sent to CCL by: &quot;S =A0Bill&quot; [S_Bill36[]<a href=3D"http://yahoo.co=
.uk" target=3D"_blank">yahoo.co.uk</a>]<br>
Dear CCL<br>
I would appraciate any references/comments/recommadtions about how to learn=
 to reparamaterize semi-empirical PM3 parameters for any ion (for example,C=
a2+). In addition to any software free or cheap for this process.<br>
Thanks in advance.<br>
S. Bill<br>
<br>
<br>
<br>
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--0016e6471b94cb72770470dd59d7--


From owner-chemistry@ccl.net Tue Aug 11 11:04:01 2009
From: "George V. Papamokos me00109|cc.uoi.gr" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL:G: Counterpoise method
Message-Id: <-39971-090811075658-2963-gG2tyRiavE0YdQF3M/CbWw-,-server.ccl.net>
X-Original-From: "George V. Papamokos" <me00109,cc.uoi.gr>
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Date: Tue, 11 Aug 2009 14:04:23 +0300
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Sent to CCL by: "George V. Papamokos" [me00109[A]cc.uoi.gr]
This is a multi-part message in MIME format.

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Dear Alessandra,

Try to download and study the papers below:
Jansen, H. B.; Ross, P. Chem. Phys. Lett. 1969, 3, 140.

Boys, S. B.; Bernardi, F. Mol. Phys. 1970, 19, 553.

They will help you understand the problem and find the formula.

Exact equations and the formula you ask can be found in the paper below:

Journal of Computational Chemistry, Vol. 22, No. 7, 765-786 (2001)



Hope I helped.



Dr.  G. V. Papamokos

Univeristy of Ioannina=20

Medical School

Ioannina 45110 =20

Panepistimioupoli Dourouti

&

Univerity of Western Macedonia

Department of Informatics and Telecommunications Engineering

Kozani 50100

Karamanli kai Lygeris Street

Greece

  ----- Original Message -----=20
  From: Alessandra Mattei ale.mattei^uky.edu=20
  To: Papamokos, George V =20
  Sent: Tuesday, August 11, 2009 12:50 AM
  Subject: CCL:G: Counterpoise method



  Sent to CCL by: "Alessandra  Mattei" [ale.mattei.[*].uky.edu]
  Dear CCL subscribers,

  I am using Counterpoise method in G03 to calculate the energy of =
intermolecular interaction between two molecules (A and B). The output =
file gives 5 energy terms: dimer (Eab), monomers with ghost functions =
(Ea* and Eb*), monomers without ghost functions(Ea and Eb) energies. At =
the end of the file there are the CP corrected energy and BSSE for the =
interaction energy. Based on these values, what is the formula to =
calculate the intermolecular energy?
  Thanks for your help.

  Alessandra Mattei
  University of Kentucky
  Department of Pharmaceutical Sciences
  725 Rose St.
  Lexington, KY 40536



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<DIV><FONT face=3D"Book Antiqua">Dear Alessandra,</FONT></DIV>
<DIV><FONT face=3D"Book Antiqua"></FONT>&nbsp;</DIV>
<DIV><FONT face=3D"Book Antiqua">Try to download and study the papers=20
below:</FONT></DIV>
<DIV>
<P align=3Dleft><FONT face=3D"Book Antiqua">Jansen, H. B.; Ross, P. =
<I>Chem. Phys.=20
Lett</I>. <B>1969</B>, <I>3</I>, 140.</FONT></P>
<P><FONT face=3D"Book Antiqua">Boys, S. B.; Bernardi, F. <I>Mol. Phys.=20
</I><B>1970</B>, <I>19</I>, 553.</FONT></P>
<P><FONT face=3D"Book Antiqua">They will help you understand the problem =
and find=20
the formula.</FONT></P>
<P><FONT face=3D"Book Antiqua">Exact equations and the formula you ask =
can be=20
found in the paper below:</FONT></P>
<P><STRONG><FONT face=3D"Book Antiqua">Journal of Computational =
Chemistry, Vol.=20
22, No. 7, 765&#8211;786 (2001)</FONT></STRONG></P>
<P><STRONG><FONT face=3D"Book Antiqua"></FONT></STRONG>&nbsp;</P>
<P><STRONG><FONT face=3D"Book Antiqua">Hope I =
helped.</FONT></STRONG></P>
<P>&nbsp;</P>
<P><FONT face=3D"Book Antiqua">Dr.&nbsp; G. V. Papamokos</FONT></P>
<P><FONT face=3D"Book Antiqua">Univeristy of Ioannina </FONT></P>
<P><FONT face=3D"Book Antiqua">Medical School</FONT></P>
<P><FONT face=3D"Book Antiqua">Ioannina 45110&nbsp; </FONT></P>
<P><FONT face=3D"Book Antiqua">Panepistimioupoli Dourouti</FONT></P>
<P><FONT face=3D"Book Antiqua">&amp;</FONT></P>
<P><FONT face=3D"Book Antiqua">Univerity of Western Macedonia</FONT></P>
<P><FONT face=3D"Book Antiqua">Department of Informatics and =
Telecommunications=20
Engineering</FONT></P>
<P><FONT face=3D"Book Antiqua">Kozani 50100</FONT></P>
<P><FONT face=3D"Book Antiqua">Karamanli kai Lygeris Street</FONT></P>
<P><FONT face=3D"Book Antiqua">Greece</FONT></P></DIV>
<BLOCKQUOTE=20
style=3D"PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; =
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
  <DIV style=3D"FONT: 10pt arial">----- Original Message ----- </DIV>
  <DIV=20
  style=3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =
black"><B>From:</B>=20
  <A title=3Downer-chemistry[*]ccl.net=20
  href=3D"mailto:owner-chemistry[*]ccl.net">Alessandra Mattei =
ale.mattei^uky.edu</A>=20
  </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>To:</B> <A =
title=3Dme00109[*]cc.uoi.gr=20
  href=3D"mailto:me00109[*]cc.uoi.gr">Papamokos, George V </A> =
</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Sent:</B> Tuesday, August 11, 2009 =
12:50=20
  AM</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Subject:</B> CCL:G: Counterpoise =
method</DIV>
  <DIV><BR></DIV><BR>Sent to CCL by: "Alessandra&nbsp; Mattei"=20
  [ale.mattei.[*].uky.edu]<BR>Dear CCL subscribers,<BR><BR>I am using =
Counterpoise=20
  method in G03 to calculate the energy of intermolecular interaction =
between=20
  two molecules (A and B). The output file gives 5 energy terms: dimer =
(Eab),=20
  monomers with ghost functions (Ea* and Eb*), monomers without ghost=20
  functions(Ea and Eb) energies. At the end of the file there are the CP =

  corrected energy and BSSE for the interaction energy. Based on these =
values,=20
  what is the formula to calculate the intermolecular energy?<BR>Thanks =
for your=20
  help.<BR><BR>Alessandra Mattei<BR>University of Kentucky<BR>Department =
of=20
  Pharmaceutical Sciences<BR>725 Rose St.<BR>Lexington, KY=20
  40536<BR><BR><BR><BR>-=3D This is automatically added to each message =
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------=_NextPart_000_0178_01CA1A8C.A1201B60--


From owner-chemistry@ccl.net Tue Aug 11 11:40:00 2009
From: "Marcel Swart marcel.swart|a|icrea.es" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: reparamaterize semi-empirical PM3 parameters
Message-Id: <-39972-090811104300-32137-EI2S5DrtCvg9CH4RwNEIUg() server.ccl.net>
X-Original-From: Marcel Swart <marcel.swart]=[icrea.es>
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Sent to CCL by: Marcel Swart [marcel.swart[-]icrea.es]

Have a look at Mopac2009, there is the PM3 Hamiltonian also
for calcium:

  Ca: (PM3): J. J. P. STEWART, J. MOL. MOD., 10, 155-164 (2004)

Quoting "S Bill S_Bill36*_*yahoo.co.uk" <owner-chemistry.:.ccl.net>:

>
> Sent to CCL by: "S  Bill" [S_Bill36[]yahoo.co.uk]
> Dear CCL
> I would appraciate any references/comments/recommadtions about how  =20
> to learn to reparamaterize semi-empirical PM3 parameters for any ion =20
>  (for example,Ca2+). In addition to any software free or cheap for  =20
> this process.
> Thanks in advance.
> S. Bill
>
>
>
> -=3D This is automatically added to each message by the mailing script =3D=
->
>
>




=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
dr. Marcel Swart

ICREA researcher at
Institut de Qu=EDmica Computacional
Universitat de Girona

Parc Cient=EDfic i Tecnol=F2gic
Edifici Jaume Casademont (despatx A-27)
Pic de Peguera 15
17003 Girona
Catalunya (Spain)

tel
+34-972-183240
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+34-972-183241
e-mail
marcel.swart.:.icrea.es
marcel.swart.:.udg.edu
web
http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372
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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D


From owner-chemistry@ccl.net Tue Aug 11 15:00:01 2009
From: "Torsten Bruhn torsten.bruhn- -mail.uni-oldenburg.de" <owner-chemistry(~)server.ccl.net>
To: CCL
Subject: CCL: TD B2-PLYP with TURBOMOLE 6.0
Message-Id: <-39973-090811145856-7688-g+bOJAsHUFZje39bJoPcpg(~)server.ccl.net>
X-Original-From: "Torsten  Bruhn" <torsten.bruhn[*]mail.uni-oldenburg.de>
Date: Tue, 11 Aug 2009 14:58:52 -0400


Sent to CCL by: "Torsten  Bruhn" [torsten.bruhn- -mail.uni-oldenburg.de]
Hi all,

is it possible to do TD B2PLYP calculations in TURBOMOLE 6.0? In the details of Grimmes papers about TD B2PLYP he mentioned an own version of the ricc module with TURBOMOLE 5.7. Is this still needed in version 6.0?

If it is possible, how should one proceed, the online manual of TURBOMOLE is not very helpful here, we only found describtions about the calculation of B2PLYP energies.

Thanks for any help/details,

Torsten


From owner-chemistry@ccl.net Tue Aug 11 15:49:00 2009
From: "Troy Wymore wymore+/-psc.edu" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: reparamaterize semi-empirical PM3 parameters
Message-Id: <-39974-090811124518-25112-FD5eaQUjUmALNAryVa0QjQ#,#server.ccl.net>
X-Original-From: Troy Wymore <wymore===psc.edu>
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Date: Tue, 11 Aug 2009 12:02:56 -0400 (EDT)
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Sent to CCL by: Troy Wymore [wymore .. psc.edu]

Hi,

While a semiempirical MO method may contain parameters for a particular 
element (Calcium was noted), it may not be particularly accurate for some 
systems.  In several cases, various researchers have re-parameterized SMO 
methods to make them accurate for specific systems.

My group has just developed a program for SMO parameterization given a 
user's reference data.  The program uses fDynamo (www.pdynamo.org) and a 
modified Genetic Algorithm library.  The input file for running these 
calculations is easy to construct.  A tutorial on how to use it will be on 
our web site sometime later this week with directions on how to download 
and install the software.

Troy Wymore
sb.nrbsc.org


From owner-chemistry@ccl.net Tue Aug 11 17:28:00 2009
From: "Pedro Salvador pedro.salvador a udg.edu" <owner-chemistry_-_server.ccl.net>
To: CCL
Subject: CCL:G: Counterpoise method
Message-Id: <-39975-090811131543-29372-xr8BkJQfHNXh0DJBtskzIA_-_server.ccl.net>
X-Original-From: Pedro Salvador <pedro.salvador!A!udg.edu>
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Sent to CCL by: Pedro Salvador [pedro.salvador(0)udg.edu]
Hi,
it depends on what you're looking for. If by "intermolecular energy" you 
mean the energy difference associated to the process
A + B --> AB
then, besides the CP-corrected energy of the dimer (EabCP, which is 
given in Gaussian as CP-corrected energy, should be less negative than 
Eab and is defined as Eab+(Ea-Ea*)+(Eb-Eb*) for each geometry ) you need 
to compute the energies of *free* monomers (Eaf, Ebf). These are not in 
general equal to Ea and Eb, except if the monomers are single atoms. 
Then the interaction energy is EabCP -Eaf -Ebf. (the energy difference 
Ea-Eaf +Eb -Ebf >0 is the relaxation energy; the energy penalty that the 
monomers pay to acomodate to the geometry of the dimer)

On the other hand, if you wish to calculate how the energy of the dimer 
is with respect to the non interacting monomers but at the fixed 
geometry they have in the dimer, then just do
Eab - Ea* -Eb*
which comes simply because the relaxation energy vanishes (or is ignored)
Pedro

Alessandra Mattei ale.mattei^uky.edu wrote:
> Sent to CCL by: "Alessandra  Mattei" [ale.mattei.%.uky.edu]
> Dear CCL subscribers,
> 
> I am using Counterpoise method in G03 to calculate the energy of intermolecular interaction between two molecules (A and B). The output file gives 5 energy terms: dimer (Eab), monomers with ghost functions (Ea* and Eb*), monomers without ghost functions(Ea and Eb) energies. At the end of the file there are the CP corrected energy and BSSE for the interaction energy. Based on these values, what is the formula to calculate the intermolecular energy?
> Thanks for your help.
> 
> Alessandra Mattei
> University of Kentucky
> Department of Pharmaceutical Sciences
> 725 Rose St.
> Lexington, KY 40536>