From owner-chemistry@ccl.net Tue Jul 9 04:03:00 2013 From: "peter john alexandre meandme_meandme2003|a|yahoo.com" To: CCL Subject: CCL:G: How to make IR spectrum from gaussian 09 Message-Id: <-48904-130709040043-22758-y9VV73FtF+AdSWXFsqitLA^-^server.ccl.net> X-Original-From: "peter john alexandre" Date: Tue, 9 Jul 2013 04:00:42 -0400 Sent to CCL by: "peter john alexandre" [meandme_meandme2003^^yahoo.com] Hi all, How can I make a IR spectrum from gaussian 09 data. Do i only extract freq/inten values from gaussian 09 log files and plot 2 columns in Excel or is there any other calculation involved before making IR spectrum. In publication, IR spectrum shows sharp single line peaks and not broad peak. How that graph is made. I have an excel file that can intake 2 column freq inten values but it changes inten. values after doing calc in excel and generating a graph. i tried using gaussview but its axis shows diff. units than freq/inten. thank you From owner-chemistry@ccl.net Tue Jul 9 07:29:00 2013 From: "Quentin Delettre quentin.delettre%%gmail.com" To: CCL Subject: CCL: Tool to generate conformer database for ligand_like molecules Message-Id: <-48905-130709025335-16899-UNx87URgxW7cVfCZQnK2iA##server.ccl.net> X-Original-From: Quentin Delettre Content-Type: multipart/alternative; boundary="------------090306060600090903030502" Date: Tue, 09 Jul 2013 09:00:20 +0200 MIME-Version: 1.0 Sent to CCL by: Quentin Delettre [quentin.delettre#gmail.com] This is a multi-part message in MIME format. --------------090306060600090903030502 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi, You can read this article : Freely Available Conformer Generation Methods: How Good Are They? * http://pubs.acs.org/doi/abs/10.1021/ci2004658 Short list of freely available tools (from the article) :Balloon, Confab, Frog2 and RDKit Commercial ones : Corina, Omega, MOE If you want to be able to customize the conformer generation workflow, i suggest you RDKit as it is a library more than a software. But Corina is the best. > > On Sat, Jul 6, 2013 at 5:01 AM, Bin Sun sunbinxod*gmail.com > > wrote: > > Hello Everyone, > > I want to achieve all the possible conformations corresponding to > the minimums on the potential surface of a ligand_like molecule. > > To this end, I firstly need to generate as many as possible > conformers by rotating the rotatable bonds via some tools or > software; Secondly, A sifting stage is performed in which the > "bad" conformers having unfavorable energies are excluded. To > ensure that there are no important conformations being omitted. > the conformer database generated in the first step must be as > completed as possible. > > Is there any tool or software that can generate completed > conformer database for ligand_like molecules ? > > Thanks ! > > -Sun > --------------090306060600090903030502 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi,

You can read this article :

Freely Available Conformer Generation Methods: How Good Are They?

http://pubs.acs.org/doi/abs/10.1021/ci2004658

Short list of freely available tools (from the article) : Balloon, Confab, Frog2 and RDKit

Commercial ones : Corina, Omega, MOE

If you want to be able to customize the conformer generation workflow, i suggest you RDKit as it is a library more than a software. But Corina is the best.


On Sat, Jul 6, 2013 at 5:01 AM, Bin Sun sunbinxod*gmail.com <owner-chemistry%a%ccl.net> wrote:
Hello Everyone,

I want to achieve all the possible conformations corresponding to the minimums on the potential surface of a ligand_like molecule.

 To this end, I firstly need to generate as many as possible conformers by rotating the rotatable bonds via some tools or software; Secondly, A sifting stage is performed in which the "bad" conformers having unfavorable energies are excluded. To ensure that there are no important conformations being omitted. the conformer database generated in the first step must  be as completed as possible. 

Is there any tool or software that can generate completed conformer database for ligand_like molecules ?

Thanks !

-Sun
--------------090306060600090903030502-- From owner-chemistry@ccl.net Tue Jul 9 08:04:00 2013 From: "peter john alexandre cumputerman{:}gmail.com" To: CCL Subject: CCL:G: How to make IR spectrum from gaussian 09 Message-Id: <-48906-130709031956-19105-E2BZrZq/yhCXlBVhgK1zuQ#%#server.ccl.net> X-Original-From: "peter john alexandre" Date: Tue, 9 Jul 2013 03:19:55 -0400 Sent to CCL by: "peter john alexandre" [cumputerman..gmail.com] Hi all, How can I make a IR spectrum from gaussian 09 data. Do i only extract freq/inten values from gaussian 09 log files and plot 2 columns in Excel or is there any other calculation involved before making IR spectrum. In publication, IR spectrum shows sharp single line peaks and not broad peak. How that graph is made. I have an excel file that can intake 2 column freq inten values but it changes inten. values after doing calc in excel and generating a graph. i tried using gaussview but its axis shows diff. units than freq/inten. thank you From owner-chemistry@ccl.net Tue Jul 9 08:39:00 2013 From: "Tal Weiss tal.the.white:_:gmail.com" To: CCL Subject: CCL:G: PES Calculation Message-Id: <-48907-130709053215-28803-RDaKMk+0R+36bm1qU+J1EQ(-)server.ccl.net> X-Original-From: "Tal Weiss" Date: Tue, 9 Jul 2013 05:32:14 -0400 Sent to CCL by: "Tal Weiss" [tal.the.white#%#gmail.com] Dear All, I am currently using GAUSSIAN 09 to scan for Potential Energy Surfaces. Since all the parameters in the z matrix are independent, I can scan one parameter (e.g. angle or bond length) and freeze the others. I didn't find however a way to scan two depended parameters. For example, Let's say the parameter B1 is given by: B1 1.1 S 10 0.01 now, I would like that parameter B2 will be B2=2*B1 at each step. (I don't want to scan them independently) Is it possible? Thanks, Tal. From owner-chemistry@ccl.net Tue Jul 9 11:35:01 2013 From: "Krisztian Niesz kniesz{}chemaxon.com" To: CCL Subject: CCL: Tool to generate conformer database for ligand_like molecules Message-Id: <-48908-130709081251-14041-jsbe+4iVfhSRyLv9GQKmvw++server.ccl.net> X-Original-From: "Krisztian Niesz" Date: Tue, 9 Jul 2013 08:12:50 -0400 Sent to CCL by: "Krisztian Niesz" [kniesz|*|chemaxon.com] Dear Sun, ChemAxon has a solution for generating conformers of ligand-like compounds. This can be accessed in Marvin Sketch. You can apply either the Dreiding or the Merck Molecular Force-field (MMFF94) for the conformer generation. The approach ensures that you will explore quite extensively the potential energy surfaces provided by these two force-fields. The conformers are returned by the program with force-field energies, sorted by default (lowest energy conformer comes first). To get a better understanding on how 3D coordinates are generated by the algorithm, please look at the following links http://www.chemaxon.com/conf/Advanced_automatic_generation_of_3D_molecular_structures.pdf The usage of the Conformer plugin is described here: http://www.chemaxon.com/marvin/help/calculations/conformation.html#conformer Sifting the "bad" conformers is mostly done by the algorithm automatically, i.e. strained bond angles, atom collisions are generally avoided by the plugin, in addition the sorting of the structures helps selecting the relevant ones. There are a few additional options that might be interesting: 1. there is a Diversity limit you can set for the conformers. This is basically an RMSD threshold to decide whether two conformers are to be considered identical 2. you might want to enumerate possible isomers (if undefined stereo centers are present) to ensure that you really explore the 3D space. You can also do this in Marvin if you go to Calculations>Isomers>Stereoisomers 3. Hyperfine option: includes an additional small MD run automatically for generated conformers, followed by an energy minimization step. Takes more time, but helps avoid hot spots I hope this helps - Appsci team > "Bin Sun sunbinxod*gmail.com" wrote: > > Sent to CCL by: Bin Sun [sunbinxod~!~gmail.com] > --047d7b5d98e5c3a60504e0cf0588 > Content-Type: text/plain; charset=ISO-8859-1 > > Hello Everyone, > > I want to achieve all the possible conformations corresponding to the > minimums on the potential surface of a ligand_like molecule. > > To this end, I firstly need to generate as many as possible conformers by > rotating the rotatable bonds via some tools or software; Secondly, A > sifting stage is performed in which the "bad" conformers having unfavorable > energies are excluded. To ensure that there are no important conformations > being omitted. the conformer database generated in the first step must be > as completed as possible. > > Is there any tool or software that can generate completed conformer > database for ligand_like molecules ? > > Thanks ! > > -Sun > > --047d7b5d98e5c3a60504e0cf0588 > Content-Type: text/html; charset=ISO-8859-1 > Content-Transfer-Encoding: quoted-printable > >
Hello Everyone,

I want to achieve all t= > he possible conformations corresponding to the minimums on the potential su= > rface of a ligand_like molecule.

=A0To= > this end, I firstly need to generate as many as possible conformers by rot= > ating the rotatable bonds via some tools or software; Secondly, A sifting s= > tage is performed in which the "bad" conformers having unfavorabl= > e energies are excluded. To ensure that there are no important conformation= > s being omitted. the conformer database generated in the first step must = > =A0be as completed as possible.=A0
>

Is there any tool or software that can gene= > rate completed conformer database for ligand_like molecules ?
iv style>
Thanks !

> > -Sun
> > --047d7b5d98e5c3a60504e0cf0588-- > > From owner-chemistry@ccl.net Tue Jul 9 12:10:00 2013 From: "Moumita Bhattacharya m.bhattacharya%a%aggiemail.usu.edu" To: CCL Subject: CCL: Charge and spin multiplicity of a positively charged metal complex Message-Id: <-48909-130709115344-17783-9BGHuwkY1fveVVdk5+YRjQ#,#server.ccl.net> X-Original-From: "Moumita Bhattacharya" Date: Tue, 9 Jul 2013 11:53:36 -0400 Sent to CCL by: "Moumita Bhattacharya" [m.bhattacharya|*|aggiemail.usu.edu] Dear All, I am trying to optimize the structure of a metal complex that has a counter anion. I was not including the counter anion in the input. The metal is diamagnetic and the metal complex is mono positively charged without the counter anion. Should I put both charge and multiplicity as 1 in the input file and run the calculation? Thanks, Moumita Bhattacharya Graduate Student From owner-chemistry@ccl.net Tue Jul 9 12:46:01 2013 From: "Veronica Ferraresi Curotto veroferraresi() gmail.com" To: CCL Subject: CCL:G: How to make IR spectrum from gaussian 09 Message-Id: <-48910-130709122523-25582-BcdEKFoDuHzNaMyqVsNQCg_+_server.ccl.net> X-Original-From: Veronica Ferraresi Curotto Content-Type: multipart/alternative; boundary=001a1133561a0c4ebf04e1169b55 Date: Tue, 9 Jul 2013 13:24:33 -0300 MIME-Version: 1.0 Sent to CCL by: Veronica Ferraresi Curotto [veroferraresi-#-gmail.com] --001a1133561a0c4ebf04e1169b55 Content-Type: text/plain; charset=ISO-8859-1 If what you want is to draw the spectrum, you can use gaussSum. http://gausssum.sourceforge.net/ 2013/7/9 peter john alexandre cumputerman{:}gmail.com < owner-chemistry++ccl.net> > > Sent to CCL by: "peter john alexandre" [cumputerman..gmail.com] > Hi all, > > How can I make a IR spectrum from gaussian 09 data. Do i only extract > freq/inten values from gaussian 09 log files and plot 2 columns in Excel or > is there any other calculation involved before making IR spectrum. > > In publication, IR spectrum shows sharp single line peaks and not broad > peak. How that graph is made. > > I have an excel file that can intake 2 column freq inten values but it > changes inten. values after doing calc in excel and generating a graph. > > i tried using gaussview but its axis shows diff. units than freq/inten. > > thank you> > > --001a1133561a0c4ebf04e1169b55 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
If what you want is to dra= w the spectrum, you can use gaussSum.
http://gausssum.sourceforge.net/


2= 013/7/9 peter john alexandre cumputerman{:}gma= il.com <owner-chemistry++ccl.net>

Sent to CCL by: "peter john alexandre" [cumputerman..gmail.com]
Hi all,

How can I make a IR spectrum from gaussian 09 data. Do i only extract freq/= inten values from gaussian 09 log files and plot 2 columns in Excel or is t= here any other calculation involved before making IR spectrum.

In publication, IR spectrum shows sharp single line peaks and not broad pea= k. How that graph is made.

I have an excel file that can intake 2 column freq inten values =A0but it c= hanges inten. values after doing calc in excel and generating a graph.

i tried using gaussview but its axis shows diff. units than freq/inten.

thank you



-=3D This is automatically added to each message by the mailing script =3D-=
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--001a1133561a0c4ebf04e1169b55-- From owner-chemistry@ccl.net Tue Jul 9 13:20:00 2013 From: "kalyan onekalyan^^^yahoo.com" To: CCL Subject: CCL: Charge and spin multiplicity of a positively charged metal complex Message-Id: <-48911-130709130616-30565-U5wW8XM+kg1oyiI5FXOQwg:-:server.ccl.net> X-Original-From: kalyan Content-Type: multipart/alternative; boundary="1679980782-917858286-1373389564=:86835" Date: Tue, 9 Jul 2013 10:06:04 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: kalyan [onekalyan*_*yahoo.com] --1679980782-917858286-1373389564=:86835 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable charge and multiplicity as 1 how come ?=C2=A0=0A=0Ayou wanna run as a catio= n ?=C2=A0=0Acould you please tell me =C2=A0the complex name ?=C2=A0=0Aif it= s Platium start from 0 1 ,0 3 , 0 5, 0 7 . anion -1 ,14 , -1 , 13=C2=A0|=0A= bi anion -1 -13 and so on .=C2=A0=0A=0A=0AMultiplicity is calculated with t= he equation: 2 S + 1 (where S =3D =CE=A3ms or more simply put, S =3D =C2=BD= (# of unpaired electrons). When all electrons are paired S =3D 0, and the m= ultiplicity =3D 2(0) + 1 =3D 1. This case is called a singlet. If a molecul= e has 1 unpaired electron S =3D +=C2=BD and 2S + 1 =3D 2, which is called a= doublet. Two unpaired electrons would result in a triplet, etc.=0A=0ABest = regards=0Akalyan kumar dhar=C2=A0=0A=0A=0A>________________________________= =0A> From: Moumita Bhattacharya m.bhattacharya%a%aggiemail.usu.edu =0A>To: "Dhar, Kalyan kumar " =0A>Sent: Tuesday, July 9, 2013 5:53 PM=0A>Subject: CCL: Charge an= d spin multiplicity of a positively charged metal complex=0A> =0A>=0A>=0A>S= ent to CCL by: "Moumita=C2=A0 Bhattacharya" [m.bhattacharya|*|aggiemail.usu= .edu]=0A>Dear All,=0A>=0A>I am trying to optimize the structure of a metal = complex that has a counter =0A>anion. I was not including the counter anion= in the input. The metal is =0A>diamagnetic and the metal complex is mono p= ositively charged without the =0A>counter anion. Should I put both charge a= nd multiplicity as 1 in the input file =0A>and run the calculation?=0A>=0A>= Thanks,=0A>Moumita Bhattacharya=0A>Graduate Student=0A>=0A>=0A>=0A>-=3D Thi= s is automatically added to each message by the mailing script =3D-=0A>To r= ecover the email address of the author of the message, please change=0A>the= strange characters on the top line to the (a) sign. You can also=0A>look up = the X-Original-From: line in the mail header.=0A>=0A>E-mail to subscribers:= CHEMISTRY(a)ccl.net or use:=0A>=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-b= in/ccl/send_ccl_message=0A>=0A>E-mail to administrators: CHEMISTRY-REQUEST(a)= ccl.net or use=0A>=C2=A0 =C2=A0 =C2=A0 http://www.ccl.net/cgi-bin/ccl/send_= ccl_message=0A>=0A=0A>=C2=A0 =C2=A0 =C2=A0 http://w= ww.ccl.net/chemistry/sub_unsub.shtml=0A>=0A>Before posting, check wait time= at: http://www.ccl.net=0A>=0A=0A>Conferences= : http://server.ccl.net/chemistry/announcements/conferences/=0A>=0A>Search = Messages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A>=0A>If your= mail bounces from CCL with 5.7.1 error, check:=0A>=C2=A0 =C2=A0 =C2=A0 htt= p://www.ccl.net/spammers.txt=0A>=0A>RTFI: http://www.ccl.net/chemistry/abou= tccl/instructions/=0A>=0A>=0A>=0A>=0A>=0A>=0A> --1679980782-917858286-1373389564=:86835 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
charge and multiplicity as 1 how come ? 
you wanna run as a cation ? 
could you please tell me &n= bsp;the complex name ? 
i= f its Platium start from 0 1 ,0 3 , 0 5, 0 7 . anion -1 ,14 , -1 , 13 = |
bi anion -1 -13 and so on . 


Multiplicity is calculated with= the equation: 2 S + 1 (where S =3D =CE=A3ms or more simply put, S =3D =C2= =BD(# of unpaired electrons). When all electrons are paired S =3D 0, and th= e multiplicity =3D 2(0) + 1 =3D 1. This case is called a singlet. If a mole= cule has 1 unpaired electron S =3D +=C2=BD and 2S + 1 =3D 2, which is calle= d a doublet. Two unpaired electrons would result in a triplet, etc.<= /div>

Best regards
kal= yan kumar dhar 
From: Moumita Bhattacharya m.bhattacharya%a%aggiemail.u= su.edu <owner-chemistry(a)ccl.net>
To: "Dhar, Kalyan kumar " <kalyan.dhar(a)mail.pol= imi.it>
Sent: Tues= day, July 9, 2013 5:53 PM
Subject= : CCL: Charge and spin multiplicity of a positively charged meta= l complex

=0A
Sent= to CCL by: "Moumita  Bhattacharya" [m.bhattacharya|*|aggiemail.usu.ed= u]
Dear All,

I am trying to optimize the structure of a metal com= plex that has a counter
anion. I was not including the counter anion in= the input. The metal is
diamagnetic and the metal complex is mono posi= tively charged without the
counter anion. Should I put both charge and = multiplicity as 1 in the input file
and run the calculation?

Tha= nks,
Moumita Bhattacharya
Graduate Student



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--1679980782-917858286-1373389564=:86835-- From owner-chemistry@ccl.net Tue Jul 9 14:53:00 2013 From: "Tapas Kar tapas.kar#usu.edu" To: CCL Subject: CCL:G: How to make IR spectrum from gaussian 09 Message-Id: <-48912-130709145147-4672-uGGOcWA0vuIQE2CVqfMRag]_[server.ccl.net> X-Original-From: Tapas Kar Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_ACE92244E11AF041B3028F75DA7B54E382B6BEC2mb01aggiesusued_" Date: Tue, 9 Jul 2013 18:51:40 +0000 MIME-Version: 1.0 Sent to CCL by: Tapas Kar [tapas.kar::usu.edu] --_000_ACE92244E11AF041B3028F75DA7B54E382B6BEC2mb01aggiesusued_ Content-Type: text/plain; charset="windows-1255" Content-Transfer-Encoding: quoted-printable Chemcraft, Gabedit (freeware) and Molekel (freeware) can also generate IR/R= aman spectra from G09 and GAMESS. Chemcraft - Graphical program for visualization of quantum ... www.chemcraftprog.com/=FD A convenient graphical program for working with quantum chemistry calculati= ons. Provides visualization of Gamess/Gaussian output files, useful utiliti= es for ... 1. Gabedit : A graphical user interface to computational chemistry ... gabedit.sourceforge.net/=FD Gabedit : A Graphical User Interface to computational chemistry packages. 1. Download Molekel Free molekel.softpedia.com/=FD Molekel description: The Molekel application was designed to be an open-sou= rce multiplatform molecular visualization program. > From: owner-chemistry+tapas.kar=3D=3Dusu.edu^ccl.net [mailto:owner-chemistr= y+tapas.kar=3D=3Dusu.edu^ccl.net] On Behalf Of Veronica Ferraresi Curotto v= eroferraresi() gmail.com Sent: Tuesday, July 09, 2013 10:25 AM To: Tapas Kar Subject: CCL:G: How to make IR spectrum from gaussian 09 If what you want is to draw the spectrum, you can use gaussSum. http://gausssum.sourceforge.net/ 2013/7/9 peter john alexandre cumputerman{:}gmail.com > Sent to CCL by: "peter john alexandre" [cumputerman..gmail.com] Hi all, How can I make a IR spectrum from gaussian 09 data. Do i only extract freq/= inten values from gaussian 09 log files and plot 2 columns in Excel or is t= here any other calculation involved before making IR spectrum. In publication, IR spectrum shows sharp single line peaks and not broad pea= k. How that graph is made. I have an excel file that can intake 2 column freq inten values but it cha= nges inten. values after doing calc in excel and generating a graph. i tried using gaussview but its axis shows diff. units than freq/inten. thank you -=3D This is automatically added to each message by the mailing script =3D-=
or u= se:E-mail to administrators: CHEMISTRY-REQUEST]-[ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtml

Chemcraft, Gabedit (freew= are) and Molekel (freeware) can also generate IR/Raman spectra from G09 and= GAMESS.

 <= /p>

Chemcraft - Graphical program for visualization of quantum ...

www.chemcraftprog.com/= =FD

A convenient graphical program for working with quantum chemistry calculations. Provides vi= sualization of Gamess/Gaussian output files, useful utilities for .= ..

 <= /p>

1.&nb= sp;  Gabe= dit : A graphical user interface to computational chemistry ...

gabedit= .sourceforge.net/=FD

Gabedit : A Graphical User Interface to computation= al chemistry packages.

 

1.&nb= sp;  Download Molekel Free

molekel= .softpedia.com/=FD

Molekel description: The Molekel application was designed to be an open-source multip= latform molecular visualization program.

 <= /p>

 <= /p>

From: owner-ch= emistry+tapas.kar=3D=3Dusu.edu^ccl.net [mailto:owner-chemistry+tapa= s.kar=3D=3Dusu.edu^ccl.net] On Behalf Of Veronica Ferraresi Curotto veroferraresi() gmail.com Sent: Tuesday, July 09, 2013 10:25 AM
To: Tapas Kar
Subject: CCL:G: How to make IR spectrum from gaussian 09<= /span>

 

If what you want is to draw the spectrum, = you can use gaussSum.
http://gausssum.sourceforge.ne= t/

 

2013/7/9 peter john alexandre cumputerman{:}gmail.com <owner-chemistry]-[ccl.net>


Sent to CCL by: "peter john alexandre" [cumputerman..gmail.com]

Hi all,

How can I make a IR spectrum from gaussian 09 data. Do i only extract freq/= inten values from gaussian 09 log files and plot 2 columns in Excel or is t= here any other calculation involved before making IR spectrum.

In publication, IR spectrum shows sharp single line peaks and not broad pea= k. How that graph is made.

I have an excel file that can intake 2 column freq inten values  but i= t changes inten. values after doing calc in excel and generating a graph.
i tried using gaussview but its axis shows diff. units than freq/inten.

thank you



-=3D This is automatically added to each message by the mailing script =3D-= <br


E-mail to subscribers: CHEMISTRY]-[c= cl.net or use:
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--_000_ACE92244E11AF041B3028F75DA7B54E382B6BEC2mb01aggiesusued_-- From owner-chemistry@ccl.net Tue Jul 9 16:10:00 2013 From: "Johannes Hachmann jh..chemistry.harvard.edu" To: CCL Subject: CCL:G: How to make IR spectrum from gaussian 09 Message-Id: <-48913-130709132550-15500-+4gZDyeX03a93fLVFd5IAQ]^[server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 9 Jul 2013 13:25:39 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh^_^chemistry.harvard.edu] Hi Peter John, There are a number of codes that can do this. Try for instance Gabedit (http://gabedit.sourceforge.net/) or Avogadro (http://avogadro.openmolecules.net/wiki/Main_Page) Good luck and best wishes, Johannes ------------------------------------------------------------------- Dr. Johannes Hachmann Research Associate Harvard University Department of Chemistry and Chemical Biology 12 Oxford St, Rm M104A Cambridge, MA 02138 ------------------------------------------------------------------- Starting 01/2014: Assistant Professor University at Buffalo The State University of New York Department of Chemical and Biological Engineering Center of Excellence in Materials Informatics Furnas Hall Buffalo, NY 14260 ------------------------------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh==chemistry.harvard.edu_+_ccl.net [mailto:owner- > chemistry+jh==chemistry.harvard.edu_+_ccl.net] On Behalf Of peter john > alexandre cumputerman{:}gmail.com > Sent: Tuesday, 09 July, 2013 03:20 > To: Hachmann, Johannes > Subject: CCL:G: How to make IR spectrum from gaussian 09 > > > Sent to CCL by: "peter john alexandre" [cumputerman..gmail.com] Hi all, > > How can I make a IR spectrum from gaussian 09 data. Do i only extract > freq/inten values from gaussian 09 log files and plot 2 columns in Excel or is > there any other calculation involved before making IR spectrum. > > In publication, IR spectrum shows sharp single line peaks and not broad peak. > How that graph is made. > > I have an excel file that can intake 2 column freq inten values but it changes > inten. values after doing calc in excel and generating a graph. > > i tried using gaussview but its axis shows diff. units than freq/inten. > > thank youTo > recover the email address of the author of the message, please change the > strange characters on the top line to the _+_ sign. You can also look up the X- > Original-From: line in the mail header. From owner-chemistry@ccl.net Tue Jul 9 16:44:01 2013 From: "Jan Labanowski janl---speakeasy.net" To: CCL Subject: CCL: CCL Admin takes vacations Jul 10-24, 2013 Message-Id: <-48914-130709162746-16306-Yg9fpY1MJl5eta30SqNE9g]*[server.ccl.net> X-Original-From: Jan Labanowski Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Tue, 09 Jul 2013 16:27:37 EDT MIME-Version: 1.0 Sent to CCL by: Jan Labanowski [janl(-)speakeasy.net] Dear CCL addicts, I will go on vacations for two weeks starting tomorrow and the server will be unattended. If s.]*[.#$ happens, then you will have a break from CCL. I will try to access the server any time I have the access to the Internet, but in some parks where I go, they say that there is "no coverage" for my Wi-Fi hub in the phone, so there will be delays. So, as always, expect unexpected.... Jan -- Jan Labanowski jkl.]*[.ccl.net CCL Admin From owner-chemistry@ccl.net Tue Jul 9 17:19:00 2013 From: "Lucus White lucus.white2000,gmail.com" To: CCL Subject: CCL: The most recent papers in computational chemistry Message-Id: <-48915-130709162606-15220-aCQCErtSYsEkiztLycb2MA|,|server.ccl.net> X-Original-From: "Lucus White" Date: Tue, 9 Jul 2013 16:26:05 -0400 Sent to CCL by: "Lucus White" [lucus.white2000[]gmail.com] Hi All, I'm just curious about what the best way is to check the latest papers. For instance, I want to see the most recent issues and the ASAP papers in the major journals. I normally visit the journal websites one by one, but is there any better way to do it? Any suggestions would be appreciated. Best wishes, Lucus lucus.white2000**gmail.com From owner-chemistry@ccl.net Tue Jul 9 17:54:01 2013 From: "=?iso-8859-1?Q?S=E9rgio_Emanuel_Galembeck?= segalemb#,#usp.br" To: CCL Subject: CCL: The most recent papers in computational chemistry Message-Id: <-48916-130709175100-16310-gtvYJwapujSrFo5NB0D/7w!^!server.ccl.net> X-Original-From: =?iso-8859-1?Q?S=E9rgio_Emanuel_Galembeck?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 9 Jul 2013 18:54:24 -0400 Mime-Version: 1.0 (Mac OS X Mail 6.5 \(1508\)) Sent to CCL by: =?iso-8859-1?Q?S=E9rgio_Emanuel_Galembeck?= [segalemb#%#usp.br] Dear Lucus, I receive in my e-mail a content alerts of the journals of my interest. You only need to go to the site of the publisher and sign this content alerts. Hope this help you, Best regards, Sergio Em 09/07/2013, ās 16:26, "Lucus White lucus.white2000,gmail.com" escreveu: > > Sent to CCL by: "Lucus White" [lucus.white2000[]gmail.com] > Hi All, > > I'm just curious about what the best way is to check the latest papers. For instance, I want to see the > most recent issues and the ASAP papers in the major journals. I normally visit the journal websites one > by one, but is there any better way to do it? > > Any suggestions would be appreciated. > > Best wishes, > Lucus > lucus.white2000,,gmail.com> > From owner-chemistry@ccl.net Tue Jul 9 20:48:01 2013 From: "Johannes Hachmann jh%%chemistry.harvard.edu" To: CCL Subject: CCL: The most recent papers in computational chemistry Message-Id: <-48917-130709182032-10814-FJWZI1aTdbEjVGPzaO0pJQ~!~server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 9 Jul 2013 18:20:24 -0400 MIME-Version: 1.0 Sent to CCL by: "Johannes Hachmann" [jh^^chemistry.harvard.edu] Hi Lucus, Try RSS feeds with some feed reader such as FeedDemon (http://www.feeddemon.com/). Whenever new papers come up in the journals you signed up for, they appear in your reader where you can search for keywords, archive and organize the ones you are interested in, and delete everything else. I find this a very convenient way to stay on top of the literature. Best wishes Johannes ----------------------------------------------- Dr. Johannes Hachmann Research Associate Harvard University Department of Chemistry and Chemical Biology 12 Oxford St, Rm M104A Cambridge, MA 02138 ----------------------------------------------- Starting 01/2014: Assistant Professor University at Buffalo The State University of New York Department of Chemical and Biological Engineering Center of Excellence in Materials Informatics Furnas Hall Buffalo, NY 14260 ----------------------------------------------- > -----Original Message----- > From: owner-chemistry+jh==chemistry.harvard.edu .. ccl.net [mailto:owner- > chemistry+jh==chemistry.harvard.edu .. ccl.net] On Behalf Of Lucus White > lucus.white2000,gmail.com > Sent: Tuesday, 09 July, 2013 16:26 > To: Hachmann, Johannes > Subject: CCL: The most recent papers in computational chemistry > > > Sent to CCL by: "Lucus White" [lucus.white2000[]gmail.com] Hi All, > > I'm just curious about what the best way is to check the latest papers. For > instance, I want to see the most recent issues and the ASAP papers in the major > journals. I normally visit the journal websites one by one, but is there any better > way to do it? > > Any suggestions would be appreciated. > > Best wishes, > Lucus > lucus.white2000,,gmail.comTo > recover the email address of the author of the message, please change the > strange characters on the top line to the .. sign. You can also look up the X- > Original-From: line in the mail header. From owner-chemistry@ccl.net Tue Jul 9 21:23:01 2013 From: "Brian Salter-Duke brian.james.duke[-]gmail.com" To: CCL Subject: CCL:G: A new email list for users of the VB2000 program Message-Id: <-48918-130709182832-17514-rqHyMoF11oPF6LdbF5wy0Q:server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Wed, 10 Jul 2013 08:28:17 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke---gmail.com] VB2000 is a general program for valence bond calculations. A new version that interfaces with Gaussian will be released soon. It is also released with GAMESS and compiled into GAMESS by default. Some CCL members may therefore be interested in this proposal. The authors of VB2000 have decided to start an informal email list for the discussion of matters related to VB2000. For the user, this will allow them to get wider assistance than asking the authors directly. For the authors it will allow us to seek assistance in things like testing the code or giving feedback on systems we have no access to. It will also allow us to announce new releases. We already have sufficient users signed up from an earlier mail out. The list will be offically started next week. We expect the list will have very low traffic. It will work by people sending an email to me, with "VB2000 List" in the Subject line. I will then forward it on to those who subscribe to the list. You will not have access to the list of subscribers. If you wish to join this list, please let me know directly. Perhaps to entice you to look at VB2000, here is the present situation. There are three versions. The version of VB2000 in the current GAMESS release can go to g orbitals and use GAMESS to calculate a range of properties from the VB wave function. Work is in progress to add the capability to use h and i orbitals, which GAMESS introduced in the current release. The original stand-alone version is limited to s, p and d orbitals. The new Gaussian version is a stand-alone program that reads data files created by Gaussian in a similar way to NBO. It does not involve compiling VB2000 and will therefore suit users who only have access to the Gaussian binaries. The Gaussian version, unlike the other versions, can use spherical harmonic basis sets directly, thus reducing the basis set size. All versions have routines to create data to use in other programs to visualise VB orbitals and recently total, VB and spin densities have been added. The centroid of charge and extent of VB orbitals are printed. The new spin-coupled method for n electrons in m orbitals has been added. Brian Duke. -- VB2000 - for all valence bond calculations. http://www.vb2000.net Brian Salter-Duke (Brian Duke) Adjunct Associate Professor Monash Institute of Pharmaceutical Sciences, Parkville Campus Monash University, Victoria, VIC 3052, Australia b_duke(0)bigpond.net.au or brian.Salter-Duke(0)monash.edu From owner-chemistry@ccl.net Tue Jul 9 21:58:01 2013 From: "Muammar El Khatib elkhatib|a|irsamc.ups-tlse.fr" To: CCL Subject: CCL: The most recent papers in computational chemistry Message-Id: <-48919-130709183737-2340-wVy+niNOuqFBnw2vsON/jQ _ server.ccl.net> X-Original-From: Muammar El Khatib Content-Type: text/plain; charset=UTF-8 Date: Wed, 10 Jul 2013 00:36:57 +0200 MIME-Version: 1.0 Sent to CCL by: Muammar El Khatib [elkhatib(0)irsamc.ups-tlse.fr] Hi, On Tue, Jul 9, 2013 at 10:26 PM, Lucus White lucus.white2000,gmail.com wrote: > Hi All, > > I'm just curious about what the best way is to check the latest papers. For instance, I want to see the > most recent issues and the ASAP papers in the major journals. I normally visit the journal websites one > by one, but is there any better way to do it? > > Any suggestions would be appreciated. > You could subscribe to a RSS service (like www.feedly.com) or install a RSS client, and then add the RSS feeds of your interest that are available in most of the journals' websites. Regards, -- Muammar El Khatib. Linux user: 403107. GPG Key = 127029F1 http://muammar.me | http://proyectociencia.org ,''`. : :' : `. `' `-