From owner-chemistry@ccl.net Thu Jun 9 10:25:00 2011 From: "harish sankar hariaimar*|*gmail.com" To: CCL Subject: CCL: Integration of weka in eclipse Message-Id: <-44870-110607010048-14377-434RaM2qmPPcJqY5UxkYmA===server.ccl.net> X-Original-From: harish sankar Content-Type: multipart/alternative; boundary=00151773dbf6e86bd204a5181990 Date: Tue, 7 Jun 2011 10:30:39 +0530 MIME-Version: 1.0 Sent to CCL by: harish sankar [hariaimar _ gmail.com] --00151773dbf6e86bd204a5181990 Content-Type: text/plain; charset=ISO-8859-1 hello abhik, i havent worked with eclipse,but from what i can make out of your question, adding the weka-src .jar file is all that is necessary. please figure out how to do it in eclipse.. On Sun, Jun 5, 2011 at 11:50 PM, Abhik Seal abhik1368[]gmail.com < owner-chemistry[a]ccl.net> wrote: > > Sent to CCL by: "Abhik Seal" [abhik1368-x-gmail.com] > How can we intergrate weka as a plugin in Eclipse enviroment . I want a > step by step guide in windows enviroment.> > > --00151773dbf6e86bd204a5181990 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable hello abhik,
=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 i havent = worked with eclipse,but from what i can make out of your question, adding t= he weka-src .jar file=A0 is all that is necessary. please figure out how to= do it in eclipse..

On Sun, Jun 5, 2011 at 11:50 PM, Abhik Seal abhik1368[]gmail.com <owner-chemistry[a]ccl.net> wrote:

Sent to CCL by: "Abhik =A0Seal" [abhik1368-x-gmail.com]
How can we intergrate weka as a plugin in Eclipse enviroment . I want a ste= p by step guide in windows enviroment.



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--00151773dbf6e86bd204a5181990-- From owner-chemistry@ccl.net Thu Jun 9 14:26:01 2011 From: "Abrash, Sam sabrash~!~richmond.edu" To: CCL Subject: CCL:G: Correctly Determining Binding Energies Using Counterpoise Message-Id: <-44871-110609142515-10068-4ckjb7FqCl7d0V3mq66nUQ!^!server.ccl.net> X-Original-From: "Abrash, Sam" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_DB1DF332AFC21544BA642BA6B7D4654D2ED57C389CUREXCHANGESCC_" Date: Thu, 9 Jun 2011 14:25:01 -0400 MIME-Version: 1.0 Sent to CCL by: "Abrash, Sam" [sabrash]^[richmond.edu] --_000_DB1DF332AFC21544BA642BA6B7D4654D2ED57C389CUREXCHANGESCC_ Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Folks, I'm about to do some calculations using the Counterpoise keyword in G09. I= need some help in calculating the binding energy of my complex from the ou= tput. I know, for example, how and where to find the counterpoise corrected= energy, and I know that the binding energy is counterpoise corrected energy of complex - counterpoise corrected energy fr= agment 1 - counterpoise corrected energy fragment 2. What I don't know is where to find the counterpoise corrected energy of the= fragments in the Gaussian 09 or Gaussian 03 output. I would greatly appre= ciate it if someone could help me with this (the Gaussian User's Reference = isn't much help since it doesn't show the output.) I would especially help= if someone could attach at least a portion of an output file which include= s the counterpoise corrected energies of the fragments and the complex, so = I can see where they are in a real case. Thank you very much for your help. Sam Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-287-1897 E-mail: sabrash]*[richmond.edu Web-page: http://www.richmond.edu/~sabrash "In 1893 Charles Hinton left Japan to become a mathematics instructor at Pr= inceton University, where he invented a baseball-pitching machine that used= gunpowder to propel the balls, like a cannon. After several accidents, th= e device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian St= eward and Jack Cohen, The Science of Diskworld III > From: owner-chemistry+sabrash=3D=3Drichmond.edu]*[ccl.net [mailto:owner-chemi= stry+sabrash=3D=3Drichmond.edu]*[ccl.net] On Behalf Of Miguel Quiliano Meza r= ifaximina=3D=3D=3Dgmail.com Sent: Tuesday, March 22, 2011 6:15 PM To: Abrash, Sam Subject: CCL: Carbocation calculations, an approach Dear colleagues. My apologies if I disturb you with a couple of questions. I have never worked with carbocations, but now I have a good case to start I would like to answer some chemicals questions using computational chemist= ry, but unfortunately I obtained rare energy values. Could you tell me please, what should I do? or what kind of chemistry model= should I use?. I want to answer some questions: *Which reaction is the most probable to happen? *What energy is necessary to reach transitional compounds before obtained p= roducts? I have performed some calculations using this: # opt=3Dtight freq b3lyp/6-31+g scf=3Dqc with the respect spin multiplicit= y, but my calculations told me that compound A is most stable than B, besid= es compound C is most stable than A and B. I stopped here because I think t= hat is impossible. A: is a carbocation very similar in structure like B B is not a carbocation C is a carbocation product of A+B Final energy for A =3D -195.60813 Final energy for B =3D -195.27260 Final energy for C =3D -390.92315 Thank in advance for your time. Maybe if you don=B4t have time please recom= men me one good paper or good tutorial. Best regards. Miguel. --_000_DB1DF332AFC21544BA642BA6B7D4654D2ED57C389CUREXCHANGESCC_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Hi Folks,

 

I’m about to do some calculations using the Counterp= oise keyword in G09.=A0 I need some help in calculating the binding energy = of my complex from the output. I know, for example, how and where to find t= he counterpoise corrected energy, and I know that the binding energy is

&nb= sp;

counter= poise corrected energy of complex – counterpoise corrected energy fra= gment 1 – counterpoise corrected energy fragment 2.=

 

What I don’t kno= w is where to find the counterpoise corrected energy of the fragments in th= e Gaussian 09 or Gaussian 03 output.=A0 I would greatly appreciate it if so= meone could help me with this (the Gaussian User’s Reference isn̵= 7;t much help since it doesn’t show the output.)=A0 I would especiall= y help if someone could attach at least a portion of an output file which i= ncludes the counterpoise corrected energies of the fragments and the comple= x, so I can see where they are in a real case.

 

Thank you very much for your help= .

 

Sam=

=  

Samu= el A. Abrash
Department of Chemistry
University of Richmond
Richmo= nd, VA 23173
Phone:=A0 804-289-8248
Fax:=A0 804-287-1897
E-mail:= =A0 sabr= ash]*[richmond.edu
Web-page:=A0 http://www.richmond.edu/~sabr= ash

"In 1893&= nbsp;Charles Hinton left Japan to become a mathematics instructor at P= rinceton University, where he invented a baseball-pitching machine tha= t used gunpowder to propel the balls, like a cannon.  After several ac= cidents, the device was abandoned and Hinton lost his job ..." Terry P= ratchett, Ian Steward and Jack Cohen, The Science of Diskworld III

&nbs= p;

From: owner-chemistry+sabras= h=3D=3Drichmond.edu]*[ccl.net [mailto:owner-chemistry+sabrash=3D=3Drichmond.e= du]*[ccl.net] On Behalf Of Miguel Quiliano Meza rifaximina=3D=3D=3Dgma= il.com
Sent: Tuesday, March 22, 2011 6:15 PM
To: Abrash= , Sam
Subject: CCL: Carbocation calculations, an approach

 

Dear colleagues.

My apologies= if I disturb you with a couple of questions.

I have never worked wi= th carbocations, but now I have a good case to start

I would like to= answer some chemicals questions using computational chemistry, but unfortu= nately I obtained rare energy values.

Could you tell me please, what= should I do? or what kind of chemistry model should I use?.

I want= to answer some questions:

*Which reaction is the most probable to h= appen?
*What energy is necessary to reach transitional compounds before = obtained products?

I have performed some calculations using this:
# opt=3Dtight freq b3lyp/6-31+g scf=3Dqc  with the respect spin m= ultiplicity, but my calculations told me that compound A is most stable tha= n B, besides compound C is most stable than A and B. I stopped here because= I think that is impossible.

A: is a carbocation very similar in str= ucture like B
 B is not a carbocation
C is a carbocation product= of A+B

Final energy for A =3D -195.60813

Final energy for B = =3D -195.27260

Final energy for C =3D -390.92315

Thank in adv= ance for your time. Maybe if you don=B4t have time please recommen me one g= ood paper or good tutorial.

Best regards.
Miguel.

= --_000_DB1DF332AFC21544BA642BA6B7D4654D2ED57C389CUREXCHANGESCC_-- From owner-chemistry@ccl.net Thu Jun 9 15:01:00 2011 From: "Prija Ponnan prija.ponnan~!~gmail.com" To: CCL Subject: CCL: Conformation search analysis for virtual screening Message-Id: <-44872-110609143024-16195-0mW+xGnL3QXqZBuDpTd3Nw%server.ccl.net> X-Original-From: Prija Ponnan Content-Type: multipart/alternative; boundary=bcaec554e06c1e31fa04a54ba5ff Date: Thu, 9 Jun 2011 12:29:38 -0600 MIME-Version: 1.0 Sent to CCL by: Prija Ponnan [prija.ponnan[*]gmail.com] --bcaec554e06c1e31fa04a54ba5ff Content-Type: text/plain; charset=ISO-8859-1 Hello all I would like to know if conformational search analysis is needed before doing virtual screening from chemical database. Thank You Prija Ponnan Research Student Department of Chemistry University of Delhi Delhi-110007, India & Canadian Commonwealth Scholarship Program Scholar College of Pharmacy and Nutrition University of Saskatchewan Saskatoon,SKN5C9,Canada --bcaec554e06c1e31fa04a54ba5ff Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello all
I would like to know if conformational search analysis is need= ed before doing virtual screening from chemical database.

Thank You<= br>
Prija Ponnan=20
=A0
Research Student
Department of Chemistry
University of Delhi
Delhi-110007, India
&
Canadian Commonwealth Scholarship Program Scholar
College of Pharmacy and Nutrition
University of Saskatchewan
Saskatoon,SKN5C9,Canada
=A0

--bcaec554e06c1e31fa04a54ba5ff-- From owner-chemistry@ccl.net Thu Jun 9 16:50:01 2011 From: "Mike F Falcetta mffalcetta(_)gcc.edu" To: CCL Subject: CCL:G: Gaussian 09; radial extent of numerical integration Message-Id: <-44873-110609164716-2098-dSixF4JXRo+/Qtb64HGetQ]~[server.ccl.net> X-Original-From: "Mike F Falcetta" Date: Thu, 9 Jun 2011 16:47:15 -0400 Sent to CCL by: "Mike F Falcetta" [mffalcetta-.-gcc.edu] Can anyone help me specify the radial extent of the numerical integration for dft calculations in gaussian 09. I know how to change the density of grid points, but I want to force the grid out to large radial extent. I have tried things like "Big Atoms", but I was looking to systematically extend the range. Thanks in advance. Mike