From owner-chemistry@ccl.net Mon Aug 30 03:50:00 2010 From: "Thishana Singh singht_-_dut.ac.za" To: CCL Subject: CCL:G: Visualization of G09 output Message-Id: <-42640-100830034912-4733-9BGHuwkY1fveVVdk5+YRjQ%%server.ccl.net> X-Original-From: Thishana Singh Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_81DF9FB413A687439AC309E7E914C8E417135AFC06SMLSMBXSTF01d_" Date: Mon, 30 Aug 2010 09:48:53 +0200 MIME-Version: 1.0 Sent to CCL by: Thishana Singh [singht:dut.ac.za] --_000_81DF9FB413A687439AC309E7E914C8E417135AFC06SMLSMBXSTF01d_ Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: quoted-printable Dear Abhishek What version of Gausview are you using to view G09 outputs ? You can view G09 output with Gausview Ver.5. If you have a lower version, the you need to upgrade. Hope this helps. Thishana Singh Department of Chemistry Durban University of Technology South Africa > From: owner-chemistry+singht=3D=3Ddut.ac.za|-|ccl.net [mailto:owner-chemistry= +singht=3D=3Ddut.ac.za|-|ccl.net] On Behalf Of Yi (Yves) Wang yves.wang * duk= e.edu Sent: 28 August 2010 08:09 PM To: Thishana Singh Subject: CCL:G: Visualization of G09 output Have you tried Gabedit and Molden? ___________________________________________________________________________= __ Yi (Yves) Wang Department of Biochemistry Structural Biology & Biophysics Program Duke University BS: University of Science and Technology of China School of Life Sciences, National Laboratory for Physical Sciences at Micro= scale Tel: +1-919-236-3307 (Cell) +1-919-684-0235 (Lab 1) +1-919-660-1634 (Lab 2) Office: A20 LSRC / 5301 FFSC E-Mail: yves.wang[*]duke.edu Mail: Box 90317, Chemistry Department =1B$B:_=1B(B 2010-8-28=1B$B!$2<8a=1B(B12:20=1B$B!$=1B(B ABHISHEK SHAHI shah= i.abhishek1984!^!gmail.com =1B$B there any free softwar= e for visualizing all results. Your suggestions will be appreciated and helpful for others too......... With regards; ABHISHEK SHAHI IISc bangalore-12 Official E-mail: shahi()ipc.iisc.ernet.in CC: shahi.abhishek1984()gmail.com ________________________________ "This e-mail is subject to our Disclaimer, to view click http://www.dut.ac.= za" --_000_81DF9FB413A687439AC309E7E914C8E417135AFC06SMLSMBXSTF01d_ Content-Type: text/html; charset="iso-2022-jp" Content-Transfer-Encoding: quoted-printable

Dear Abhishek

 

What version of Gausview are you using to view G09 outputs ?=

You can view G09 output with Gausview Ver.5.

If you have a lower version, the you need to upgrade.

Hope this helps.

 

Thishana Singh

Department of Chemistry

Durban University of Technology

South Africa

 

From: owner-ch= emistry+singht=3D=3Ddut.ac.za|-|ccl.net [mailto:owner-chemistry+singh= t=3D=3Ddut.ac.za|-|ccl.net] On Behalf Of Yi (Yves) Wang yves.wang * duke.edu
Sent: 28 August 2010 08:09 PM
To: Thishana Singh
Subject: CCL:G: Visualization of G09 output

 

Have you tried Gabedit and Molden?

____________________________________________________________= _________________

 

Yi (Yves) Wang

Department of Biochemistry

Structural Biology & Biophysics Program

Duke University

BS: University of Science and Technology of China=

School of Life Sciences, National Laboratory for Physical Sc= iences at Microscale

Tel: +1-919-236-3307 (Cell)

   +1-919-684-0235 (Lab 1)

   +1-919-660-1634 (Lab 2)

Office: A20 LSRC / 5301 FFSC

Mail: Box 90317, Chemistry Department

 

=1B$B:_=1B(B 2010-8-28=1B$B!$2<8a=1B(B12:20=1B$B!$= =1B(B ABHISHEK SHAHI shahi.abhishek1984!^!gmail.com =1B$B



Dear All

&= nbsp;  I am facing problem in visualizing G09 output. Gaussview= (not reading vibration),Avagadro (not reading optimisation steps),chemcraf= t(not reading vibration and optimization steps).These all were suitable for G03 output.Please suggest me that what should I do.Is there any free software for visualizing all results.

&= nbsp;Your suggestions will be  appreciated and helpful fo= r=   others too.........









With regards;
 ABHISHEK SHAHI
&= nbsp; IISc bangalore-12
&= nbsp; Official E-mail: shahi()ipc.iisc.ernet.in
&= nbsp; CC:  shahi.ab= hishek1984()gmail.com

 


"This e-mail is subject= to our Disclaimer, to view click http://www.dut.ac.za"
 --_000_81DF9FB413A687439AC309E7E914C8E417135AFC06SMLSMBXSTF01d_-- From owner-chemistry@ccl.net Mon Aug 30 08:51:00 2010 From: "Hans De Winter hans.dewinter[#]silicos.com" To: CCL Subject: CCL: Release of SIEVE v3 as open source package Message-Id: <-42641-100830050448-416-n0OlqXn2RMUKM7DSWvAiIg_._server.ccl.net> X-Original-From: Hans De Winter Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Mon, 30 Aug 2010 11:04:36 +0200 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Hans De Winter [hans.dewinter]_[silicos.com] Dear all, Silicos NV, a Belgian-based company providing services in the field of computational chemistry and drug design, has released SIEVE version 3.0.1 as open source code under the terms of the GNU GPL as published the Free Software Foundation version 2 of the License. SIEVE is a program for filtering out molecules with unwanted properties. It is based on the Open Babel open source C++ API for rapid calculation of molecular properties. The program comes with a number of pre-programmed molecular properties that can be used for filtering. These properties include, amongst others: * Physicochemical parameters, such as logP, topological polar surface area criteria, number of hydrogen bond acceptors and donors, and Lipinski's rule-of-five; * Graph-based properties, including ring-based parameters and rotatable bond criteria; * Selection criteria by means of smarts patterns; * Similarity criteria; * Three-dimensional distances between user-definable fragments. SIEVE is a command line-driven program that is instructed by means of command line options and a user-definable filter file. Please visit Silicos' website at www.silicos.com for more details, download instructions and documentation. Kind regards, Hans De Winter Silicos NV From owner-chemistry@ccl.net Mon Aug 30 11:01:00 2010 From: "Sayed Mesa elsayed.elmes]_[yahoo.com" To: CCL Subject: CCL: BSSE Counterpoise correction for A + B + C------> D +E reaction Message-Id: <-42642-100830105939-30696-ErhtLqpQ3RUhTY96KsJ1Tg(!)server.ccl.net> X-Original-From: "Sayed Mesa" Date: Mon, 30 Aug 2010 10:59:38 -0400 Sent to CCL by: "Sayed Mesa" [elsayed.elmes^_^yahoo.com] Dear CCL community If you have a reaction like [M2L]4+ + CO2 + MeOH ----> [M2LMeCO3]3+ + H+ where M is a transition metal and L is a chelate ligand, how I can calculate the BSSE for this type of reaction. I know how I can calculate the BSSE for A + B ---> C reaction but I do not know for A + B + C------> D +E reaction. Could anyone help me? Thanks in advance Saye From owner-chemistry@ccl.net Mon Aug 30 11:45:00 2010 From: "Bachrach, Steven STEVEN.BACHRACH]_[Trinity.edu" To: CCL Subject: CCL:G: Visualization of G09 output Message-Id: <-42643-100830100144-7496-I0wan5JuQk9EydnR84yNPA~!~server.ccl.net> X-Original-From: "Bachrach, Steven" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_DE6997A61EEABE4A86FA984E284258B205825B3430ITSBlancotrin_" Date: Mon, 30 Aug 2010 09:01:33 -0500 MIME-Version: 1.0 Sent to CCL by: "Bachrach, Steven" [STEVEN.BACHRACH[]Trinity.edu] --_000_DE6997A61EEABE4A86FA984E284258B205825B3430ITSBlancotrin_ Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: quoted-printable You actually DO NOT HAVE to upgrade your version of GaussView just to visua= lization vibrations from a G-09 output. I contacted Gaussian about the inab= ility to view vibrations generated in G-09 within non-GaussView v5.0. The s= olution is simple: The formatted read of the output file is particular for the white space. Wi= thin the G-09 output file, change every occurrence of =1B$B!H=1B(BAtom AN=1B$B!I=1B(B to =1B$B!H=1B(BAtom AN=1B$B!I=1B(B (note the 2 spaces between =1B$B!F=1B(Bm=1B$B!G=1B(B and =1B$B!F=1B(BA=1B$B= !G=1B(B now becomes just 1 space) Don=1B$B!G=1B(Bt you just love formatted read calls? Steven Steven Bachrach, Chair ph: (210)999-7379 Department of Chemistry fax: (210)999-7569 Trinity University 1 Trinity Place San Antonio, TX 78212 steven.bachrach=trinity.edu > From: owner-chemistry+steven.bachrach=3D=3Dtrinity.edu=ccl.net [mailto:owne= r-chemistry+steven.bachrach=3D=3Dtrinity.edu=ccl.net] On Behalf Of Thishana= Singh singht_-_dut.ac.za Sent: Monday, August 30, 2010 2:49 AM To: Bachrach, Steven Subject: CCL:G: Visualization of G09 output Dear Abhishek What version of Gausview are you using to view G09 outputs ? You can view G09 output with Gausview Ver.5. If you have a lower version, the you need to upgrade. Hope this helps. Thishana Singh Department of Chemistry Durban University of Technology South Africa > From: owner-chemistry+singht=3D=3Ddut.ac.za::ccl.net [mailto:owner-chemistr= y+singht=3D=3Ddut.ac.za::ccl.net] On Behalf Of Yi (Yves) Wang yves.wang * d= uke.edu Sent: 28 August 2010 08:09 PM To: Thishana Singh Subject: CCL:G: Visualization of G09 output Have you tried Gabedit and Molden? ___________________________________________________________________________= __ Yi (Yves) Wang Department of Biochemistry Structural Biology & Biophysics Program Duke University BS: University of Science and Technology of China School of Life Sciences, National Laboratory for Physical Sciences at Micro= scale Tel: +1-919-236-3307 (Cell) +1-919-684-0235 (Lab 1) +1-919-660-1634 (Lab 2) Office: A20 LSRC / 5301 FFSC E-Mail: yves.wang[*]duke.edu Mail: Box 90317, Chemistry Department =1B$B:_=1B(B 2010-8-28=1B$B!$2<8a=1B(B12:20=1B$B!$=1B(B ABHISHEK SHAHI shah= i.abhishek1984!^!gmail.com =1B$B there any free softwar= e for visualizing all results. Your suggestions will be appreciated and helpful for others too......... With regards; ABHISHEK SHAHI IISc bangalore-12 Official E-mail: shahi()ipc.iisc.ernet.in CC: shahi.abhishek1984()gmail.com ________________________________ "This e-mail is subject to our Disclaimer, to view click http://www.dut.ac.= za" --_000_DE6997A61EEABE4A86FA984E284258B205825B3430ITSBlancotrin_ Content-Type: text/html; charset="iso-2022-jp" Content-Transfer-Encoding: quoted-printable

You actually DO NOT HAVE to upgrade your version of GaussVie= w just to visualization vibrations from a G-09 output. I contacted Gaussian a= bout the inability to view vibrations generated in G-09 within non-GaussView v5.= 0. The solution is simple:

 

The formatted read of the output file is particular for the = white space. Within the G-09 output file, change every occurrence of  <= /o:p>

=1B$B!H=1B(BAtom  AN=1B$B!I=1B(B to =1B$B!H=1B(BAtom AN= =1B$B!I=1B(B

(note the 2 spaces between =1B$B!F=1B(Bm=1B$B!G=1B(B and =1B= $B!F=1B(BA=1B$B!G=1B(B now becomes just 1 space)

 

Don=1B$B!G=1B(Bt you just love formatted read calls?

 

Steven

 

 

Steven Bachrach, Chair               ph: (210)999-7379

Department of Chemistry          fax: (210)9= 99-7569

Trinity University           = ;                 &nb= sp; 

1 Trinity Place

San Antonio, TX 78212

steven.bachra= ch=trinity.edu

 

 

From: owner-chemistry+steven.bachrach=3D=3Dtrinity.edu=ccl.net [mailto:owner-chemistry+steven.bachrach=3D=3Dtrinity.edu=ccl.net] On Beh= alf Of Thishana Singh singht_-_dut.ac.za
Sent: Monday, August 30, 2010 2:49 AM
To: Bachrach, Steven
Subject: CCL:G: Visualization of G09 output

 

Dear Abhishek

 

What version of Gausview are you using to view G09 outputs ?=

You can view G09 output with Gausview Ver.5.

If you have a lower version, the you need to upgrade.

Hope this helps.

 

Thishana Singh

Department of Chemistry

Durban University of Technology

South Africa

 

From: owner-chemistry+singht=3D=3Ddut.ac.za::ccl.net [mailto:owner-chemistry+singht=3D=3Ddut.ac.za::ccl.net] On Behalf Of Yi (Yves) Wang yves.wang * duke.edu
Sent: 28 August 2010 08:09 PM
To: Thishana Singh
Subject: CCL:G: Visualization of G09 output

 

Have you tried Gabedit and Molden?

____________________________________________________________= _________________

 

Yi (Yves) Wang

Department of Biochemistry

Structural Biology & Biophysics Program

Duke University

BS: University of Science and Technology of China=

School of Life Sciences, National Laboratory for Physical Sciences at Microscale

Tel: +1-919-236-3307 (Cell)

   +1-919-684-0235 (Lab 1)<= /p>

   +1-919-660-1634 (Lab 2)<= /p>

Office: A20 LSRC / 5301 FFSC

Mail: Box 90317, Chemistry Department

 

=1B$B:_=1B(B 2010-8-28=1B$B!$2<8a=1B(B12:20=1B$B!$=1B(B ABHISHEK SHAHI shahi.abhishek1984!^!gmail.= com =1B$B

 

Dear All

   I= am facing problem in visualizing G09 output. Gaussview (not reading vibration),Avagadro (not reading optimisation steps),chemcraft(not reading vibration and optimization steps).These all were suitable for G03 output.Pl= ease suggest me that what should I do.Is there any = free software for visualizing all results.

 Your suggestions will be&n= bsp; appreciated and helpful for  others too.........









With regards;
&nbs= p;ABHISHEK SHAHI
  IISc bangalore-12
  Officia= l E-mail: shahi= ()ipc.iisc.ernet.in
  CC:  shahi.abhis= hek1984()gmail.com

 

=  

"This e-mail is subject to our Disclaimer, to view click http://www.dut.ac.za"

--_000_DE6997A61EEABE4A86FA984E284258B205825B3430ITSBlancotrin_-- From owner-chemistry@ccl.net Mon Aug 30 15:51:00 2010 From: "Kalju Kahn kalju]|[chem.ucsb.edu" To: CCL Subject: CCL: Drug design: couple of education questions Message-Id: <-42644-100830154254-31492-KSvuA2Sy/W+X/LkBREO++g_-_server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 30 Aug 2010 12:42:46 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju ~~ chem.ucsb.edu] Dear all, I am trying to put together a proposal for a new drug design textbook, and thought that CCL members might have useful opinions to help me in choosing the best path. I do have a general philosophy and outline already, so I am not really asking what the book should be about :) Rather, I'd like to hear: 1) From people in industry ... what they feel is the weak point in the education of a typical university-trained pharmacology / medicinal chemistry / biochemistry student as far as drug discovery is concerned? 2) From computational community who teaches / participates in teaching drug design classes ... is there a strong interest in ready-made on-line tutorials / practicals based on freely available software? Or would you rather implement a tutorial / practical that a textbook suggests using your own favorite commercial software suite? 3) From anyone who is in charge of teaching such a class ... either at university or corporate level ... how happy are you with your existing textbook(s)? Would an introductory text with extensive breath and moderate depth catch your interest? Best regards, Kalju ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Mon Aug 30 16:44:00 2010 From: "Chris Swain swain%%mac.com" To: CCL Subject: CCL: Drug design: couple of education questions Message-Id: <-42645-100830164213-30597-zeWVVErZ5dVyHHFTyza1eQ-x-server.ccl.net> X-Original-From: Chris Swain Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Mon, 30 Aug 2010 21:41:34 +0100 MIME-version: 1.0 Sent to CCL by: Chris Swain [swain#%#mac.com] Hi, I've been a tutor for the RSC MedChem Course for a number of years and here are few thoughts. Sadly textbooks seem outdated pretty quickly, and I suspect they are only really useful as an introduction. The RSC course we give is updated every two years. I'm not convinced that hard copy is the way forward. I was approached about writing a book and instead decided on web publishing (http://homepage.mac.com/swain/CMC/DDResources/DDResources.html) which means I can add to and update regularly (well I try to do it regularly!). For the next RSC course we are thinking of recording the lectures/tutorials and making them available, perhaps on iTunesU, so that people can follow them at their own pace. We were thinking of using tools that are freely available or accessible via web service. Perhaps using http://www.vcclab.org/ for physicochemical properties. However I do think one of the most valuable part of the meeting is giving the participants the opportunity to quiz the presenters. Case histories are very popular, I compare and contrast 3 or 4 groups different approaches to the same target. Cheers, Chris On 30 Aug 2010, at 20:42, Kalju Kahn kalju]|[chem.ucsb.edu wrote: > > Sent to CCL by: "Kalju Kahn" [kalju ~~ chem.ucsb.edu] > Dear all, > > I am trying to put together a proposal for a new drug design textbook, > and thought that CCL members might have useful opinions to help me in > choosing the best path. I do have a general philosophy and outline > already, so I am not really asking what the book should be about :) > Rather, I'd like to hear: > > 1) From people in industry ... what they feel is the weak point in the > education of a typical university-trained pharmacology / medicinal > chemistry / biochemistry student as far as drug discovery is concerned? > > 2) From computational community who teaches / participates in teaching > drug design classes ... is there a strong interest in ready-made on-line > tutorials / practicals based on freely available software? Or would you > rather implement a tutorial / practical that a textbook suggests using your > own favorite commercial software suite? > > 3) From anyone who is in charge of teaching such a class ... either at > university or corporate level ... how happy are you with your existing > textbook(s)? Would an introductory text with extensive breath and > moderate depth catch your interest? > > Best regards, > > Kalju > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr. Kalju Kahn > Department of Chemistry and Biochemistry > UC Santa Barbara, CA 93106> > From owner-chemistry@ccl.net Mon Aug 30 17:18:00 2010 From: "Marcel Swart marcel.swart^-^icrea.es" To: CCL Subject: CCL:G: Visualization of G09 output Message-Id: <-42646-100830125204-16386-j8ppfD0XmOM3I47Sop+tSQ-#-server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-2--62771711 Date: Mon, 30 Aug 2010 18:51:46 +0200 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Marcel Swart [marcel.swart=-=icrea.es] --Apple-Mail-2--62771711 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=windows-1252 For those who are unfamiliar with the "sed" (stream editor), the = following command should do the trick: sed 's/Atom AN/Atom AN/g' < XX.log > XXgv.log where XX.log is the old output, and XXgv.log is the one that should = work. Marcel. On Aug 30, 2010, at 4:01 PM, Bachrach, Steven = STEVEN.BACHRACH]_[Trinity.edu wrote: > You actually DO NOT HAVE to upgrade your version of GaussView just to = visualization vibrations from a G-09 output. I contacted Gaussian about = the inability to view vibrations generated in G-09 within non-GaussView = v5.0. The solution is simple: > =20 > The formatted read of the output file is particular for the white = space. Within the G-09 output file, change every occurrence of =20 > =93Atom AN=94 to =93Atom AN=94 > (note the 2 spaces between =91m=92 and =91A=92 now becomes just 1 = space) > =20 > Don=92t you just love formatted read calls? > =20 > Steven > =20 > =20 > Steven Bachrach, Chair ph: (210)999-7379 > Department of Chemistry fax: (210)999-7569 > Trinity University =20 > 1 Trinity Place > San Antonio, TX 78212 > steven.bachrach-x-trinity.edu =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 Research Professor 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 fax +34-972-183241 e-mail marcel.swart+/-icrea.es marcel.swart+/-udg.edu web http://www.marcelswart.eu =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 --Apple-Mail-2--62771711 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=windows-1252 For = those who are unfamiliar with the "sed" (stream editor), the = following
command should do the = trick:

sed 's/Atom  AN/Atom AN/g'  < =  XX.log  > =  XXgv.log

where XX.log = is the old output, and XXgv.log is the one that should = work.

Marcel.

On Aug = 30, 2010, at 4:01 PM, Bachrach, Steven STEVEN.BACHRACH]_[Trinity.edu = wrote:

You actually DO NOT HAVE to upgrade your version of = GaussView just to visualization vibrations from a G-09 output. I = contacted Gaussian about the inability to view vibrations generated in = G-09 within non-GaussView v5.0. The solution is = simple:
The formatted read of = the output file is particular for the white space. Within the G-09 = output file, change every occurrence of =  
=93Atom  AN=94 to = =93Atom AN=94
(note the 2 spaces = between =91m=92 and =91A=92 now becomes just 1 = space)
Don=92t you just love = formatted read calls?
Steven Bachrach, = Chair           =     ph: (210)999-7379
Department of = Chemistry          fax: = (210)999-7569
Trinity = University          &nbs= p;     =             &n= bsp; 
1 Trinity = Place
San Antonio, TX = 78212




= --Apple-Mail-2--62771711-- From owner-chemistry@ccl.net Mon Aug 30 17:53:00 2010 From: "Johannes Salewski Johannes.Salewski+/-tu-berlin.de" To: CCL Subject: CCL:G: gaussian produces lots of imaginary frequencies Message-Id: <-42647-100830123118-29061-DcLZ7yM/kzDFN/rwjvF1hw]![server.ccl.net> X-Original-From: Johannes Salewski Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 30 Aug 2010 18:31:07 +0200 MIME-Version: 1.0 Sent to CCL by: Johannes Salewski [Johannes.Salewski-.-tu-berlin.de] Dear all, I use gaussian09 or 03 to calculate the vibrational frequencies of a protein chromophore. For approx. 25 slightly different (in geometry) structures I receive 14-16 negative (imaginary) frequencies for each calculation without exception. I could not find or think of any error in the input files. Can somebody give me a hint, where a possible reason for this could be found? If more information is needed, I will provide is asap. Thank you very much, Johannes Salewski, Berlin, Germany From owner-chemistry@ccl.net Mon Aug 30 18:28:01 2010 From: "Eduard Matito ematito%a%gmail.com" To: CCL Subject: CCL:G: AIM2000 pi electron population Message-Id: <-42648-100830123711-7955-/MWbWL/AsRsw0laBZtNizA:-:server.ccl.net> X-Original-From: Eduard Matito Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Mon, 30 Aug 2010 18:36:57 +0200 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Eduard Matito [ematito..gmail.com] Dear Sagarika, I haven't used AIM2000 for a while but, if you have available the atomic overlap matrix (AOM) there, it should be easy to retrieve the pi population. Simply sum the diagonal terms of the AOM for those orbitals of pi symmetry. If you cannot find AOM try using other software which provides such matrix, e.g. Bader's group software (AIMPAC). http://www.chemistry.mcmaster.ca/aimpac/ In Istvan Mayer's webpage you will find some software to perform energy decomposition analysis. http://occam.chemres.hu/programs/ Best, Eduard On Aug 27, 2010, at 7:53 AM, Sagarika Dev sagarika.dev,gmail.com wrote: > > Sent to CCL by: "Sagarika Dev" [sagarika.dev-,-gmail.com] > Dear All, > Could you please inform me if there is any option in AIM2000 > package to calculate sigma and pi electron population of an atom? I > am able to find out the total electron population of an atom by > integration over atomic basin. My aim is to find out the tranfer of > pi and sigma electron separately from one monomer to another after > stacking. Is it possible to do so? > > My second question is is there any freeware through which I can > decompose my interaction energy in physically relevant counterparts- > like-electrostatic, dispersion etc; I have access to G03 and I am > looking for some freeware either in windows or in linux where I can > use the output from G03. > > Any help will be highly appreciated. > > Regards > Sagarika > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > -- Eduard Matito Postdoctoral researcher Institute of Physics University of Szczecin Wielkopolska 15 70451 Szczecin (Poland) Phone: +48914441436 http://ematito.webs.com From owner-chemistry@ccl.net Mon Aug 30 19:03:00 2010 From: "Damian Bikiel dbikiel!=!qi.fcen.uba.ar" To: CCL Subject: CCL:G: gaussian produces lots of imaginary frequencies Message-Id: <-42649-100830180508-2087-0VWsJTv4lzsK8bcFsMsvJA_-_server.ccl.net> X-Original-From: Damian Bikiel Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: Text/Plain; charset="iso-8859-1" Date: Mon, 30 Aug 2010 19:04:48 -0300 MIME-Version: 1.0 Sent to CCL by: Damian Bikiel [dbikiel-x-qi.fcen.uba.ar] Are your structures optimized? the frequencies of a structure which is not a minimum in the potential energy surface is meaningless. damian On Lunes 30 Agosto 2010 13:31:07 Johannes Salewski Johannes.Salewski+/-tu- berlin.de wrote: > Sent to CCL by: Johannes Salewski [Johannes.Salewski-.-tu-berlin.de] > Dear all, > > I use gaussian09 or 03 to calculate the vibrational frequencies of a > protein chromophore. > For approx. 25 slightly different (in geometry) structures I receive > 14-16 negative (imaginary) frequencies for each calculation without > exception. I could not find or think of any error in the input files. > Can somebody give me a hint, where a possible reason for this could be > found? > If more information is needed, I will provide is asap. > > Thank you very much, > Johannes Salewski, > Berlin, Germany-- Dr. Damian Bikiel Grupo de Modelado Molecular Laboratorio de Química Organometálica DQIAQyF-INQUIMAE, FCEyN, UBA From owner-chemistry@ccl.net Mon Aug 30 19:52:01 2010 From: "Close, David M. CLOSED(~)mail.etsu.edu" To: CCL Subject: CCL:G: gaussian produces lots of imaginary frequencies Message-Id: <-42650-100830195016-9321-+6dIZnIywd82lAI0YKX35A||server.ccl.net> X-Original-From: "Close, David M." Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 30 Aug 2010 23:50:04 +0000 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED!^!mail.etsu.edu] Johannes: I don't know what structure you are working with, but there are some preliminary things to consider. First of all, is the frequency calculation on an optimized structure? Next, one needs to know if the imaginary frequencies have small values, say less than 300 cm-1, or they large, say like normal IR stretching frequencies of 1500 cm-1? If the imaginary frequencies are small, then you have to decide if this is normal or not. Sometimes small frequencies can be associated with rotations of something like a methyl group. So perhaps you have some more information on this? Regards, Dave Close. -----Original Message----- > From: owner-chemistry+closed==etsu.edu]=[ccl.net [mailto:owner-chemistry+closed==etsu.edu]=[ccl.net] On Behalf Of Johannes Salewski Johannes.Salewski+/-tu-berlin.de Sent: Monday, August 30, 2010 12:31 PM To: Close, David M. Subject: CCL:G: gaussian produces lots of imaginary frequencies Sent to CCL by: Johannes Salewski [Johannes.Salewski-.-tu-berlin.de] Dear all, I use gaussian09 or 03 to calculate the vibrational frequencies of a protein chromophore. For approx. 25 slightly different (in geometry) structures I receive 14-16 negative (imaginary) frequencies for each calculation without exception. I could not find or think of any error in the input files. Can somebody give me a hint, where a possible reason for this could be found? If more information is needed, I will provide is asap. Thank you very much, Johannes Salewski, Berlin, Germanyhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt