From owner-chemistry@ccl.net Thu Mar 18 09:32:01 2010 From: "Mr. Satyajit Sarmah satyacs,,tezu.ernet.in" To: CCL Subject: CCL: How to get the value of Laplacian at different points Message-Id: <-41492-100318020711-32357-Rg7AWE5wGrpbwAxLYO2/Jw!A!server.ccl.net> X-Original-From: "Mr. Satyajit Sarmah" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 18 Mar 2010 11:36:43 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Mr. Satyajit Sarmah" [satyacs^^^tezu.ernet.in] Hi I am using AIMALL. I want to know how to get the value of Laplacian at different points along a bond path using AIMALL or any other such packages. If someone can suggest in this regard. Thanks. Satyajit. ___________________ D I S C L A I M E R This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. Though considerable effort has been made to deliver error free e-mail messages but it can not be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, delayed, or may contain viruses. The recipient must verify the integrity of this e-mail message. From owner-chemistry@ccl.net Thu Mar 18 10:07:01 2010 From: "Partha Biswas partha361~~gmail.com" To: CCL Subject: CCL:G: fixing charges on atom in gaussian03 package Message-Id: <-41493-100316072312-18184-kOzC4J0BcAaMiIYkXvMrLA/./server.ccl.net> X-Original-From: "Partha Biswas" Date: Tue, 16 Mar 2010 07:23:08 -0400 Sent to CCL by: "Partha Biswas" [partha361,,gmail.com] am an user of Gaussian03 package. I want to specify charges on atoms. The overall charge of the molecule is 0 but for molecules such as amino acid which I want to be in zwitterionic form that is the amine (-NH2) group will be NH3+ and the carboxylic acid (-COOH) group will stay as COO-. Thus I have to specify the charge on nitrogen atom (N) as +1 and oxygen atom (O) of COO- group as -1. After that I will run the full optimization (with keyword fopt) in gas phase. Though gas phase amino acid zwitterion is not stable and it will actually transform to neutral form, but if I can fix charges then probably not transform to its neutral from. I will be helpful if you kindly help me out of this problem. From owner-chemistry@ccl.net Thu Mar 18 10:42:01 2010 From: "Curt Breneman brenec]![rpi.edu" To: CCL Subject: CCL: Emerging Technologies in Computational Chemistry Award Symposium - Boston ACS Meeting Message-Id: <-41494-100317215729-8255-UK+IxeeK4I6oLJ1mTW0pgA]![server.ccl.net> X-Original-From: "Curt Breneman" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_0047_01CAC616.0B4B12D0" Date: Wed, 17 Mar 2010 21:08:50 -0400 MIME-Version: 1.0 Sent to CCL by: "Curt Breneman" [brenec*_*rpi.edu] This is a multi-part message in MIME format. ------=_NextPart_000_0047_01CAC616.0B4B12D0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Call for Papers: 2010 Symposium on Emerging Technologies in Computational Chemistry at the American Chemical Society National Meeting, Boston, MA Aug. 22-26 2010 >>>> Note: The Deadline for COMP Abstracts for the Boston meeting is March 20th, 2010 <<<< $1,000 prize to be awarded at the ACS national meeting, Boston, MA. In cooperation with Schrodinger, Inc, the Computers in Chemistry Division (COMP) of the ACS will hold the annual Symposium on Emerging Technologies in Computational Chemistry at the American Chemical Society National Meeting, Boston, MA, Aug. 22-26 2010. The objective of the symposium is to stimulate, reward, and publicize methodological advances in computational chemistry. The talks will be evaluated at the meeting by a panel of experts on the quality of the presentation, and the impact that the research will have on the future of computational chemistry and allied sciences. The symposium is ideal for presenting your latest and best research on new techniques, applications and software development. Schrodinger, Inc., sponsors a $1,000 prize for the best talk at the symposium. All are invited to participate. To take part, it is necessary to submit a regular short ACS abstract the PACS system. It is also necessary to also email a longer (~1000-word) abstract to the organizer. The talks must be original and not be repeats of talks at other ACS symposia. The long abstracts will be evaluated, and those individuals selected for an oral presentation at the symposium will be notified. Applications for the Emerging Technologies Symposium that cannot be accepted will be rescheduled in one of the other COMP sessions at the meeting. Long abstracts must be sent by e-mail to: Prof. Curt M. Breneman Chair, ACS Division of Computers in Chemistry Acting Head, RPI Department of Chemistry and Chemical Biology Brenec_at_rpi_dot_edu ------=_NextPart_000_0047_01CAC616.0B4B12D0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Call for Papers: 2010 Symposium on Emerging = Technologies in Computational Chemistry at the = American Chemical Society National Meeting, Boston, MA

Aug. 22-26 2010

 

>>>> Note: The Deadline for COMP = Abstracts for the Boston meeting is March 20th, 2010 = <<<<

 

$1,000 prize to be awarded at the ACS = national meeting, Boston, MA.

 

In cooperation with Schrodinger, Inc, the Computers = in Chemistry Division (COMP) of the ACS

will hold the annual Symposium on Emerging = Technologies in Computational Chemistry at the

American Chemical Society National Meeting, Boston, = MA, Aug. 22-26

2010. The objective of the symposium is to = stimulate, reward, and publicize

methodological advances in computational = chemistry.

 

The talks will be evaluated at the meeting by a = panel of experts on the

quality of the presentation, and the impact that = the research will have on

the future of computational chemistry and allied = sciences. The symposium is

ideal for presenting your latest and best research = on new techniques,

applications and software = development.

 

Schrodinger, Inc., sponsors a $1,000 prize for the = best talk at the

symposium.

 

All are invited to participate. To take part, it is necessary to submit a

regular short ACS abstract the PACS system. It is = also necessary

to also email a longer (~1000-word) abstract to the organizer. The talks

must be original and not be repeats of talks at = other ACS symposia. The long

abstracts will be evaluated, and those individuals = selected for an oral

presentation at the symposium will be notified. = Applications for the

Emerging Technologies Symposium that cannot be = accepted will be rescheduled

in one of the other COMP sessions at the = meeting.

 

Long abstracts must be sent by e-mail = to:

 

Prof. Curt M. Breneman

Chair, ACS Division of Computers in = Chemistry

Acting Head, RPI Department of Chemistry and = Chemical Biology

Brenec_at_rpi_dot_edu

 

 

 

 

------=_NextPart_000_0047_01CAC616.0B4B12D0-- From owner-chemistry@ccl.net Thu Mar 18 13:54:00 2010 From: "Ivo Jacobs jacobs.ivo|a|gmail.com" To: CCL Subject: CCL:G: fixing charges on atom in gaussian03 package Message-Id: <-41495-100318112448-16896-x+qlvR4iHXLAHxW+hDs8HA,,server.ccl.net> X-Original-From: Ivo Jacobs Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 18 Mar 2010 15:58:29 +0100 MIME-Version: 1.0 Sent to CCL by: Ivo Jacobs [jacobs.ivo(~)gmail.com] Partha Biswas partha361~~gmail.com wrote: > am an user of Gaussian03 package. I want to specify charges on atoms. The > overall charge of the molecule is 0 but for molecules such as amino acid which > I want to be in zwitterionic form that is the amine (-NH2) group will be NH3+ > and the carboxylic acid (-COOH) group will stay as COO-. Thus I have to specify > the charge on nitrogen atom (N) as +1 and oxygen atom (O) of COO- group as -1. > After that I will run the full optimization (with keyword fopt) in gas phase. > Though gas phase amino acid zwitterion is not stable and it will actually > transform to neutral form, but if I can fix charges then probably not transform > to its neutral from. > > I will be helpful if you kindly help me out of this problem. You don't have to specify the charges in this case. As long as you put the proton where you want it, so on the nitrogen, Gaussian will distribute the electrons properly, resulting in a positive charge on the nitrogen, and a negative charge on the oxygen. Unless the proton is very close to the oxygen it will not go back to the oxygen automatically. HTH Ivo From owner-chemistry@ccl.net Thu Mar 18 16:26:00 2010 From: "Shirin Seifert shirin.seifert : gmail.com" To: CCL Subject: CCL: ONIOM Problem Message-Id: <-41496-100318115818-28402-yp320a2WOGSuUhiCtcU13A_._server.ccl.net> X-Original-From: Shirin Seifert Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 18 Mar 2010 18:19:12 +0330 MIME-Version: 1.0 Sent to CCL by: Shirin Seifert [shirin.seifert .. gmail.com] Hello : I have a similar porblem as Arash' post bellow. Any suggestions would be appreciated. Thank you. S.Seifert Hi All, I have a molecular system with two cations. I have tried ONIOM with the following line in the route section. However this does not generate any surface (HOMO) in gaussview when opening the checkpoint file. Thanks for your suggestions in advance ******************************************************************************* #p oniom(uhf/sto-3g*:uhf/sto-3g*) nosymm charge 1 2 1 2 1 2 ; two molecules with unity charge on each ; Two Cation structures with layers H & L point charges ******************************************************************************* Thanks a lot. AR