From owner-chemistry@ccl.net Mon Sep 13 04:20:01 2010 From: "Gkourmpis, Thomas Thomas.Gkourmpis:+:borealisgroup.com" To: CCL Subject: CCL:G: formchk of .chk file Message-Id: <-42745-100913041844-5218-TgxvOZtq55jQeyuUnv6xjA/a\server.ccl.net> X-Original-From: "Gkourmpis, Thomas" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 13 Sep 2010 10:18:29 +0200 MIME-Version: 1.0 Sent to CCL by: "Gkourmpis, Thomas" [Thomas.Gkourmpis(-)borealisgroup.com] Hi Dave Have a look through this tutorial http://www.gaussian.com/g_whitepap/remote.htm on how to use Gaussian results on different machines. I hope this is helpful Thomas -----Original Message----- > From: owner-chemistry+thomas.gkourmpis==borealisgroup.com,+,ccl.net [mailto:owner-chemistry+thomas.gkourmpis==borealisgroup.com,+,ccl.net] On Behalf Of David Hose Anthrax_brothers^^hotmail.com Sent: Friday, September 10, 2010 10:29 PM To: Gkourmpis, Thomas Subject: CCL:G: formchk of .chk file Sent to CCL by: "David Hose" [Anthrax_brothers(a)hotmail.com] David, A quick look through the CCL archives suggests that you should convert the .chk to the .fchk on the same machine that created the .chk file. http://www.ccl.net/chemistry/resources/messages/2008/04/03.003-dir/index.html http://www.ccl.net/cgi-bin/ccl/message-new?2008+04+06+005 http://www.ccl.net/chemistry/resources/messages/2005/06/13.003-dir/index.html Hope these posts can help you sort out your problem. Regards, Dave. ============== Sent to CCL by: "David Close" [closed__etsu.edu] I have finished a normal Gaussian calculation and have information in a .chk file I would like to use. The Gaussian utility Formchk does not read the .chk file. Instead I get a segmentation error. Also I can not read the .chk file in GaussView. Does anyone know what to do to generate a usable .chk file?http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Sep 13 08:44:01 2010 From: "turker akcay turkerakcay{}hotmail.com" To: CCL Subject: CCL:G: Gaussian Message-Id: <-42746-100913055000-10773-qaeKozl9AY4FkotT/B5GBQ,+,server.ccl.net> X-Original-From: "turker akcay" Date: Mon, 13 Sep 2010 05:50:00 -0400 Sent to CCL by: "turker akcay" [turkerakcay() hotmail.com] Hi everybody I'm new gaussian user and I use gaussian 03 for win. I am studying on TD DFT study a dinitrile compound. After 6 days processing, because of electricity cutting, my gaussian job is terminated and computer is closed. I want to resumption my job but I dont know how do it. is it possible? or should I open latest out file and restart process. My input file; %chk=C:/Users/TURKR/Desktop/tddft50trs.chk %mem=100MW %nproc=1 #p td=(singlets,nstates=50) b3lyp/6-311+g(d) guess=save geom=connectivity pop=full gfinput final part of my out file; Cannot handle 2e integral symmetry, ISym2E=1. CISAX: IP= 1 NPass= 3 NMax= 34. CISAX will form 34 AO SS matrices at one time. NMat= 34 NSing= 34. NMat= 34 NSing= 34. NMat= 32 NSing= 32. Cannot handle 2e integral symmetry, ISym2E=1. CISAX: IP= 1 NPass= 3 NMax= 34. CISAX will form 34 AO SS matrices at one time. NMat= 34 NSing= 34. NMat= 34 NSing= 34. NMat= 32 NSing= 32. Root 1 has converged. Root 2 has converged. Root 3 has converged. Root 4 has converged. Root 5 has converged. Root 6 has converged. Root 7 has converged. Root 8 has converged. Root 9 has converged. Root 10 has converged. Root 11 has converged. Root 12 has converged. Root 13 not converged, maximum delta is 0.001146383849072 Root 14 not converged, maximum delta is 0.001076901825947 Root 15 has converged. Root 16 has converged. Root 17 has converged. Root 18 has converged. Root 19 has converged. Root 20 has converged. Root 21 has converged. Root 22 has converged. Root 23 has converged. Root 24 has converged. Root 25 has converged. Root 26 has converged. Root 27 has converged. Root 28 not converged, maximum delta is 0.001298203075257 Root 29 has converged. Root 30 has converged. Root 31 has converged. Root 32 not converged, maximum delta is 0.001487599984012 Root 33 not converged, maximum delta is 0.002130187054738 Root 34 not converged, maximum delta is 0.009687228977448 Root 35 not converged, maximum delta is 0.014708674044360 Root 36 has converged. Root 37 not converged, maximum delta is 0.001056178564194 Root 38 not converged, maximum delta is 0.001307476560090 Root 39 not converged, maximum delta is 0.001281081401660 Root 40 has converged. Root 41 not converged, maximum delta is 0.001061548241041 Root 42 not converged, maximum delta is 0.001573623655971 Root 43 has converged. Root 44 has converged. Root 45 has converged. Root 46 has converged. Root 47 not converged, maximum delta is 0.001567486009780 Root 48 not converged, maximum delta is 0.005544365303514 Root 49 not converged, maximum delta is 0.015140942251070 Root 50 not converged, maximum delta is 0.016487405708613 Excitation Energies [eV] at current iteration: Root 1 : 3.097975009587616 Change is -0.000001105943253 Root 2 : 3.583514852565895 Change is -0.000007448515000 Root 3 : 3.617241820182027 Change is -0.000021813870515 Root 4 : 3.991502586858061 Change is -0.000023174927667 Root 5 : 4.138876536189863 Change is -0.000007145969739 Root 6 : 4.211283026540273 Change is -0.000007302963600 Root 7 : 4.270327709174773 Change is -0.000012531626331 Root 8 : 4.368328284874000 Change is -0.000005937553695 Root 9 : 4.445535867701103 Change is -0.000032779976579 Root 10 : 4.540640063389401 Change is -0.000002225280201 Root 11 : 4.656404960218242 Change is -0.000023209382109 Root 12 : 4.714797549284374 Change is -0.000019602079988 Root 13 : 4.754991510970658 Change is -0.00001 From owner-chemistry@ccl.net Mon Sep 13 09:46:00 2010 From: "Reynier Suard az reynier.suardiaz||gmail.com" To: CCL Subject: CCL: generating conformations in five-membered rings Message-Id: <-42747-100913094333-918-Ub3JzeBAgFsxQFm5Y56opA||server.ccl.net> X-Original-From: "Reynier Suard az" Date: Mon, 13 Sep 2010 09:43:32 -0400 Sent to CCL by: "Reynier Suard az" [reynier.suardiaz]-[gmail.com] Dear All I would like to study the conformational dependance of certain properties in furanose rings. I would like to generate a lot of permitted conformations of the five-membered ring and calculate this property for each structure but dihedrals are coupled and I can not change one dihedral angle in this ring without afecting the others. The problem seems not be trivial. Does anybody can recomend me a software to generate controlled (not aleatory) conformations of five-membered furanose ring? or a relatively simple way to programming it? any sugestion or comment would be profoundly apreciated Best regards Reynier From owner-chemistry@ccl.net Mon Sep 13 11:48:00 2010 From: "Hans De Winter hans.dewinter*_*silicos.com" To: CCL Subject: CCL:G: Pharao: PHARmacophore Alignment and Optimization (open source) Message-Id: <-42748-100913095159-8154-NqbpWkqXMbyMWorbU45NQA**server.ccl.net> X-Original-From: "Hans De Winter" Date: Mon, 13 Sep 2010 09:51:57 -0400 Sent to CCL by: "Hans De Winter" [hans.dewinter],[silicos.com] Silicos NV, a Belgian-based company providing services in the field of computational chemistry and drug design, has released PHARAO version 3.0.0 as open source code under the terms of the GNU GPL as published the Free Software Foundation version 2 of the License. PHARAO is a program for the generation and alignment of pharmacophores calculated from small drug-like molecules. Pharmacophores are automatically generated from molecules, and include aromatic, lipophilic, charged, hydrogen bond acceptor and donor centers represented as Gaussian volumes. Alignment between pairs of pharmacophores is done by optimizing the overlap volumes of the corresponding pharmacophore Gaussians. Exclusion volumes can be taken into account as well. PHARAO has been written using Open Babels C++ API and is a command line-driven program instructed by means of command line options. 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 Sep 13 13:21:00 2010 From: "John McKelvey jmmckel##gmail.com" To: CCL Subject: CCL:G: Gaussian Message-Id: <-42749-100913122304-13129-TdA+LrDU596r+QK4aypBYA~~server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 13 Sep 2010 12:22:57 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel\a/gmail.com] Turker, First, I am not a Gaussian expert so I can not address that aspect of your query. Thoughts.. Of the first 27 states 25 are converged and you probably have good estimates of the first 12, and decent estimates for many of the remainder. Of course not having converged means that the transition moments and oscillator strengths are missing. Would you consider it useful to get first only the first 10-15 states or so on the first pass, assuming that the job is not restartable? Should run reasonably on your machine I would guess in a day or two and would give info on whether it would be necessary to get a lot more. Just a thought... John McKelvey On Mon, Sep 13, 2010 at 5:50 AM, turker akcay turkerakcay{}hotmail.com wrote: > > Sent to CCL by: "turker  akcay" [turkerakcay() hotmail.com] > Hi everybody > I'm new gaussian user and I use gaussian 03 for win. I am studying on TD DFT > study a dinitrile compound. After 6 days processing, because of electricity > cutting, my gaussian job is terminated and computer is closed. I want to > resumption my job but I dont know how do it. is it possible? or should I open > latest out file and restart process. > > My input file; > %chk=C:/Users/TURKR/Desktop/tddft50trs.chk > %mem=100MW > %nproc=1 > #p td=(singlets,nstates=50) b3lyp/6-311+g(d) guess=save geom=connectivity > pop=full gfinput > > final part of my out file; > >  Cannot handle 2e integral symmetry, ISym2E=1. >  CISAX:  IP=  1 NPass=   3 NMax=  34. >  CISAX will form  34 AO SS matrices at one time. >  NMat= 34 NSing= 34. >  NMat= 34 NSing= 34. >  NMat= 32 NSing= 32. >  Cannot handle 2e integral symmetry, ISym2E=1. >  CISAX:  IP=  1 NPass=   3 NMax=  34. >  CISAX will form  34 AO SS matrices at one time. >  NMat= 34 NSing= 34. >  NMat= 34 NSing= 34. >  NMat= 32 NSing= 32. >  Root      1 has converged. >  Root      2 has converged. >  Root      3 has converged. >  Root      4 has converged. >  Root      5 has converged. >  Root      6 has converged. >  Root      7 has converged. >  Root      8 has converged. >  Root      9 has converged. >  Root     10 has converged. >  Root     11 has converged. >  Root     12 has converged. >  Root     13 not converged, maximum delta is    0.001146383849072 >  Root     14 not converged, maximum delta is    0.001076901825947 >  Root     15 has converged. >  Root     16 has converged. >  Root     17 has converged. >  Root     18 has converged. >  Root     19 has converged. >  Root     20 has converged. >  Root     21 has converged. >  Root     22 has converged. >  Root     23 has converged. >  Root     24 has converged. >  Root     25 has converged. >  Root     26 has converged. >  Root     27 has converged. >  Root     28 not converged, maximum delta is    0.001298203075257 >  Root     29 has converged. >  Root     30 has converged. >  Root     31 has converged. >  Root     32 not converged, maximum delta is    0.001487599984012 >  Root     33 not converged, maximum delta is    0.002130187054738 >  Root     34 not converged, maximum delta is    0.009687228977448 >  Root     35 not converged, maximum delta is    0.014708674044360 >  Root     36 has converged. >  Root     37 not converged, maximum delta is    0.001056178564194 >  Root     38 not converged, maximum delta is    0.001307476560090 >  Root     39 not converged, maximum delta is    0.001281081401660 >  Root     40 has converged. >  Root     41 not converged, maximum delta is    0.001061548241041 >  Root     42 not converged, maximum delta is    0.001573623655971 >  Root     43 has converged. >  Root     44 has converged. >  Root     45 has converged. >  Root     46 has converged. >  Root     47 not converged, maximum delta is    0.001567486009780 >  Root     48 not converged, maximum delta is    0.005544365303514 >  Root     49 not converged, maximum delta is    0.015140942251070 >  Root     50 not converged, maximum delta is    0.016487405708613 >  Excitation Energies [eV] at current iteration: >  Root      1 :     3.097975009587616   Change is   -0.000001105943253 >  Root      2 :     3.583514852565895   Change is   -0.000007448515000 >  Root      3 :     3.617241820182027   Change is   -0.000021813870515 >  Root      4 :     3.991502586858061   Change is   -0.000023174927667 >  Root      5 :     4.138876536189863   Change is   -0.000007145969739 >  Root      6 :     4.211283026540273   Change is   -0.000007302963600 >  Root      7 :     4.270327709174773   Change is   -0.000012531626331 >  Root      8 :     4.368328284874000   Change is   -0.000005937553695 >  Root      9 :     4.445535867701103   Change is   -0.000032779976579 >  Root     10 :     4.540640063389401   Change is   -0.000002225280201 >  Root     11 :     4.656404960218242   Change is   -0.000023209382109 >  Root     12 :     4.714797549284374   Change is   -0.000019602079988 >  Root     13 :     4.754991510970658   Change is   -0.00001>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel{=}gmail.com From owner-chemistry@ccl.net Mon Sep 13 13:56:00 2010 From: "Rajagopala Reddy Seelam rajagopalaseelam{:}gmail.com" To: CCL Subject: CCL: Renner - Teller effect in polyatomic molecules reg Message-Id: <-42750-100913132135-9370-UGblJhHCRhLlm/aY0tUb9g**server.ccl.net> X-Original-From: "Rajagopala Reddy Seelam" Date: Mon, 13 Sep 2010 13:21:34 -0400 Sent to CCL by: "Rajagopala Reddy Seelam" [rajagopalaseelam|gmail.com] Respected CCL members, I am looking for literature on Renner - Teller effect in polyatomic molecules. The RT effect in tri atomic molecules is well documented and for tetra atomic molecules very few. A through search with Google, I could not find any paper on penta atomic or more.atomic molecules. Can any of you suggest me in this regard. Thank you From owner-chemistry@ccl.net Mon Sep 13 21:34:00 2010 From: "Abrash, Sam sabrash%x%richmond.edu" To: CCL Subject: CCL: Renner - Teller effect in polyatomic molecules reg Message-Id: <-42751-100913162118-13445-tg5YG542XPFpq0EYTT4AdQ^_^server.ccl.net> X-Original-From: "Abrash, Sam" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 13 Sep 2010 16:21:07 -0400 MIME-Version: 1.0 Sent to CCL by: "Abrash, Sam" [sabrash#%#richmond.edu] The reason for the lack of information is that the Renner-Teller effect is limited to linear molecules. The analogous effect for non-linear molecules is the Jahn-Teller effect, which is well documented for tetra-atomic molecules and larger polyatomic molecules. A good book that introduces these effects is Fischer's book entitled Vibronic Coupling. I hope this helps. Sam Samuel A. Abrash Department of Chemistry University of Richmond Richmond, VA 23173 Phone: 804-289-8248 Fax: 804-287-1897 E-mail: sabrash%a%richmond.edu Web-page: http://www.richmond.edu/~sabrash "In 1893 Charles Hinton left Japan to become a mathematics instructor at Princeton University, where he invented a baseball-pitching machine that used gunpowder to propel the balls, like a cannon.  After several accidents, the device was abandoned and Hinton lost his job ..." Terry Pratchett, Ian Steward and Jack Cohen, The Science of Diskworld III -----Original Message----- > From: owner-chemistry+sabrash==richmond.edu%a%ccl.net [mailto:owner-chemistry+sabrash==richmond.edu%a%ccl.net] On Behalf Of Rajagopala Reddy Seelam rajagopalaseelam{:}gmail.com Sent: Monday, September 13, 2010 1:22 PM To: Abrash, Sam Subject: CCL: Renner - Teller effect in polyatomic molecules reg Sent to CCL by: "Rajagopala Reddy Seelam" [rajagopalaseelam|gmail.com] Respected CCL members, I am looking for literature on Renner - Teller effect in polyatomic molecules. The RT effect in tri atomic molecules is well documented and for tetra atomic molecules very few. A through search with Google, I could not find any paper on penta atomic or more.atomic molecules. Can any of you suggest me in this regard. Thank youhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt