From owner-chemistry@ccl.net Tue Sep 23 05:52:00 2008 From: "Yangsoo Kim vsmember*_*gmail.com" To: CCL Subject: CCL:G: HR problem with G03: Problem with the number of degrees of freedom Message-Id: <-37784-080923053556-2310-3Nj2zZwvCfCCfgRczsR8PQ,server.ccl.net> X-Original-From: "Yangsoo Kim" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 23 Sep 2008 17:40:18 +0900 MIME-Version: 1.0 Sent to CCL by: "Yangsoo Kim" [vsmember:+:gmail.com] Dear All, A while ago, I posted a problem on hindered rotor calculation with G03, which is the one that other users also have. The related CCL posts on the problems are attached below. Basically, G03 terminated with the error message "Problem with the number of degrees of freedom", when molecules other than alkane are calculated for hindered rotor analysis. I wonder if there is any clue that has been posted or found. I would greatly appreciate if any one of you provides any clue to solve this problem. If this is under correction for now and there is no solution at this time > from G03 side, is there any other program that I can use for automatic HR identification and calculation for thermo property estimation? Many thanks in advance, Yangsoo Kim ================================================================ CCL:G: Hinderedrotor Problem in Gaussian03 .. From: "Greef, T.F.A. de" .. Subject: CCL:G: Hinderedrotor Problem in Gaussian03 .. Date: Tue, 6 Nov 2007 11:10:50 +0100 > From: owner-chemistry(!)ccl.net [mailto:owner-chemistry(!)ccl.net] Sent: Tuesday, November 06, 2007 9:51 AM To: Greef, T.F.A. de Subject: CCL:G: Hinderedrotor Problem in Gaussian03 Dear CCL members, I am trying to use the "HF/6-31G* opt freq=hinderedrotor" keyword in Gaussian03 to correct the themochemical data for contributions of internal rotation. It is normally terminated to calculate the hindered rotor analysis for the normal alkyl-chained systems. But I met the following error messages for various alkyl-substitutied benzene ring systems. (e.q. toluene, ethylbenzene or propylbenzene) === Error Message (propylbenzene) === Hindered Internal Rotation Analysis Internal coordinate list checked Check for planar centers 1 2 3 10 360.000 2 1 6 7 359.984 3 1 4 11 360.000 4 3 5 12 360.000 5 4 6 13 360.000 6 2 5 14 360.000 Check reduced barrier height. Cut-off : V/RT = 33.7561 Check for ring deformation Number of internal rotation degrees of freedom = 3 NNew= 48 NTest= 3 NB= 9 IFrz= 0 IBar= 0 ICyc= 0 Problem with the number of degrees of freedom Error termination... ====================== Does anyone have any suggestions to solve these problems? And please tell me another softwares to calculate the hindered rotor. Thanks in advance. Yangsoo Kim ----------------------------------------------------------------------- CCL:G: g03 Problem with "HinderedRotor" calculations ________________________________________ .. From: Ulrich Scharfenort .. Subject: CCL:G: g03 Problem with "HinderedRotor" calculations .. Date: Fri, 07 Mar 2008 11:22:51 +0100 ________________________________________ Sent to CCL by: Ulrich Scharfenort [scharfenort=ltt.rwth-aachen.de] Hello, I hope maybe one of you can help me with an problem. Currently i try to calculate Aromatic compounds with the HinderedRotor option. With Alkanes HR works very fine and without any problem so I think it's not an problem with the coordinates. The error-message is as follows: Number of internal rotation degrees of freedom = 4 NNew= 30 NTest= 4 NB= 10 IFrz= 0 IBar= 0 ICyc= 0 Problem with the number of degrees of freedom Error termination via Lnk1e in /opt/GAUSSIAN/LINUX_amd64/g03.d02/l716.exe at Fri Mar 7 11:10:19 2008. Job cpu time: 0 days 0 hours 0 minutes 15.4 seconds. File lengths (MBytes): RWF= 17 Int= 0 D2E= 0 Chk= 10 Scr= 1 This was a calculation for Butylbenzene where are internal rotations. Does HR only work for Alkanes and nothing else? Maybe somebody does know for which compound classes HR works and for which not or and way to make it working for all compounds. I will appreciate all the help you can provide on this problem. Yours sincerely ; Ulrich Scharfenort ---------------------------------------------------------------------- CCL:G: Hindered Rotor Gaussian03 ________________________________________ .. From: "Tom F.A. de Greef" .. Subject: CCL:G: Hindered Rotor Gaussian03 .. Date: Thu, 18 Jan 2007 04:38:20 -0500 ________________________________________ Sent to CCL by: "Tom F.A. de Greef" [t.f.a.d.greef ~ tue.nl] Dear all, I want to report some deltaG values generated by a Gaussian03 job on a molecule of about 20 heavy atoms (B3LYP,6_311G+(d,p). However, I want to check if the assumptian that Gaussian03 makes are correct (the free rotor assumption). I requested a fequency job using the optimised geometry at the before mentioned level using these keywords: freq=hindered rb3lyp/6-311+g(d,p) geom=(connectivity,modredundant) "Geometry in Cartesian coordinates" It computes all the derivatives and computes the full mass-weighted force constant matrix. The calculation then starts a hindered rotation analysis: Internal coordinate list checked Check for planar centers 1 2 4 27 359.993 2 1 9 28 359.996 3 4 5 8 359.927 4 1 3 29 359.965 5 3 6 15 360.000 7 8 11 12 359.998 8 3 7 9 360.000 9 2 8 10 359.998 10 9 11 13 360.000 11 7 10 14 359.994 15 5 18 21 359.928 16 17 20 33 359.996 17 16 18 34 359.993 18 15 17 35 359.965 19 20 23 25 360.000 20 16 19 21 359.998 21 15 20 22 360.000 22 21 23 24 359.999 23 19 22 26 359.993 Check reduced barrier height. Cut-off : V/RT = 33.7561 Bond 3 - 5 frozen. Estimated reduced barrier height : V/RT = 37.5137 For a periodicity of : 2 Bond 5 - 15 frozen. Estimated reduced barrier height : V/RT = 37.5712 For a periodicity of : 2 Check for ring deformation Number of internal rotation degrees of freedom = 2 NNew= 92 NTest= 2 NB= 24 IFrz= 0 IBar= 2 ICyc= 0 Problem with the number of degrees of freedom Error termination via Lnk1e in /usr/opt/gaussian/g03/l716.exe I know that the method used by Gaussian03 to correct for hindered rotation is not always working (for example it works for butane but fails for methanol). For underlying thheory: P.Y. Ayala & H.B. Schlegel, JCP 108,2314 Best regards, Tom de Greef ------------------------------------------------------------------ CCL:G: Guassian - Hindered rotor frequency option ________________________________________ .. From: "Rob Noble-Eddy" .. Subject: CCL:G: Guassian - Hindered rotor frequency option .. Date: Fri, 9 Nov 2007 09:34:04 -0500 ________________________________________ Sent to CCL by: "Rob Noble-Eddy" [r.noble-eddy^-^ed.ac.uk] Hi, I have a molecule which contains a phenyl group, and want to calculate the free energies of its two conformers. The barrier to rotation of the phenyl group is around kT and so I believe any estimation of the free energy should include this rotation, rather than simply using a standard frequency calculation on the equilibrium position. I tried to use the freq=hinderedrotor option in gaussian '03 to achieve this, but after successfully completing a geometry optimisation it starts to do the frequency calculation, but stops with an error when it tries to determine if there are any hindered rotors in the molecule. I've included the output below, if anyone has any ideas, or has used this feature before please get in touch. Thanks, Rob ============================================ Internal coordinate list checked Check for planar centers 1 2 3 7 359.997 2 1 4 9 360.000 3 1 5 10 360.000 4 2 6 11 360.000 5 3 6 12 360.000 6 4 5 13 360.000 Check reduced barrier height. Cut-off : V/RT = 33.7561 Check for ring deformation Number of internal rotation degrees of freedom = 2 NNew= 36 NTest= 2 NB= 8 IFrz= 0 IBar= 0 ICyc= 0 Problem with the number of degrees of freedom Error termination via Lnk1e in /usr/local/Chem-Apps/g03_d01/g03/l716.exe at Fri Nov 9 11:29:03 2007. ------------------------------------------------------------ CCL:G: How to Identify and correct for Hindered Rotors in G03 ________________________________________ .. From: akef afaneh .. Subject: CCL:G: How to Identify and correct for Hindered Rotors in G03 .. Date: Fri, 23 Nov 2007 06:37:39 -0800 (PST) ________________________________________ Sabry; I do not know if I can help you to solve your problem or not. However, I need more information about your job to give you a suitable example. What I see here from the output massage is that the problem in the constrained mode # 2, so, the program gave you a message to redo the normal mode analysis with added constraints. You have also a problem in the number of degrees of freedom, these usually result when a certain degree of symmetry is used and the Gaussian recognizes another symmetry. When we study a TS species with unrecognized bond, Geom=Modify keyword is usually used. Akef -------------------------------------------------------------------- Hello CCLers, I'm trying to correct for hindered rotation modes using the keyword Freq=HinderedRotor in G03. In fact I have no idea how to do that; I mean the identification and the correction. For the reactant the job terminated successfully but I don't know what I should get from the output. Fot the TS, the job failed with the following error message: ---------------------------------------------------------------------------- ----- Check correspondance between vibrational and internal rotation modes frequencies in cm**-1 1 2 3 Frequencies --- 95.0468 155.4019 177.3364 -1474.4902 0.0101 0.0562 -0.0333 92.0838 -0.9973 0.4231 0.6332 136.3765 -0.2606 0.8307 0.3015 155.3244 0.4631 -0.8491 -0.9191 195.3921 -0.6826 0.4576 0.8660 343.8586 - 0.8442 0.7230 0.8824 ---------------------------------------------------------------------------- One-to-one correspondance not acheived Constrained mode 2 likely source of the problem Bond # Atoms 1 1 2 0.00000 2 2 3 0.07105 3 3 8 0.12548 4 8 9 0.74224 Freeze coordinate 27 Freeze coordinate 28 Freeze coordinate 29 Freeze coordinate 30 Redo normal mode analysis with added constraints Number of internal rotation degrees of freedom = 3 NNew= 7 NTest= 3 NB= 4 IFrz= 1 IBar= 1 ICyc= 0 Problem with the number of degrees of freedom Error termination via Lnk1e in C:\G03W\l716.exe at Sat Nov 10 22:37:32 2007. ---------------------------------------------------------------------------- ---------------------------------------------------- I don't understand what the message means. I shall be very grateful if anyone can help me (using a simple example would be fine) Thank you in advance. Sabry Ahmed -- Sabry El-Taher Ahmed Cairo University Faculty of Science Department of Chemistry Cairo, Egypt. --------------------------------------------------------------- Hindered Rotor Analysis in G03 ________________________________________ .. From: Matthias Lein .. Subject: Hindered Rotor Analysis in G03 .. Date: Mon, 28 Jun 2004 11:17:34 +0200 ________________________________________ Hi all, investigating a molecule of 72 atoms I calculated the thermodynamical data of dissociation given by standard frequency analysis of Gaussian98 (and G03). Given one rotational barrier of about 10 kcal/mol I thought it to be useful to try the "Freq(HinderedRotor)"-Keyword in Gaussian to correct the data for contributions of internal rotation. I used an already finished harmonic frequency analysis and the "readfc"-keyword to avoid recalculation of the frequencies. The algorithm of Schlegel et al. found two internal rotations but then skipped the calculation with the following lines: > Check for ring deformation > Number of internal rotation degrees of freedom = 2 > NNew= 156 NTest= 2 NB= 45 IFrz= 0 IBar= 7 ICyc= 0 > Problem with the number of degrees of freedom > Error termination via Link716 My questions: 1) Does anyone know the limitations of this keyword? (No of atoms, degrees of freedom,...) 2) Is there knowledge about problems and performance of this method, including numerical values (is it necessary or reasonable to use these corrections)? Thanks in advance Matthias. From owner-chemistry@ccl.net Tue Sep 23 08:59:00 2008 From: "Gustavo L.C. Moura gustavo#,#mercury.chem.pitt.edu" To: CCL Subject: CCL: SUMMARY: Program for INDO/S calculations Message-Id: <-37785-080923085740-9637-WT59BJ7dlYHA+Z4ZGdYi7A|server.ccl.net> X-Original-From: "Gustavo L.C. Moura" Date: Tue, 23 Sep 2008 08:57:36 -0400 Sent to CCL by: "Gustavo L.C. Moura" [gustavo**mercury.chem.pitt.edu] Dear CCL Readers, last week I sent a message to the list inquiring about a program for performing INDO/S calculations with certain specifications. I have received three suggestions of codes that I am quoting below: 1-Jeff Reimers' (at U. Sydney, Australia) CNDO code which also does INDO/S (http://www.chem.usyd.edu.au/~reimers/); 2-David Yaron (at Carnegie Mellon) has his own INDO/S code; 3-Christopher Cramer has a code called ZINDO-MN for such calculations. Thank you for all the suggestions I have received. Sincerely yours, Dr. Gustavo L.C. Moura gustavo /at/ mercury.chem.pitt.edu ORIGINAL MESSAGE: Dear CCL Readers, I am looking for a program that performs INDO/S calculations and has the following specifications: 1- the program should be able to handle very large excitation windows in the CIS calculations. I have met serious problems with the program I am using right now. When I try to run calculations with large numbers of occupied/unoccupied orbitals the program simply refuses to perform the calculations. 2- the program should print the dipole moments of the excited states and the transition dipole moments between excited states. I want to calculate the nonlinear optical properties of organic molecules and I need these dipole moments in my calculations. Thank you very much in advance for your answers to my question. Sincerely yours, Dr. Gustavo L.C. Moura gustavo /at/ mercury.chem.pitt.edu From owner-chemistry@ccl.net Tue Sep 23 09:33:00 2008 From: "Kostas Sakellaris ksakell,+,chem.uoa.gr" To: CCL Subject: CCL:G: Gaussian Solvent Optimization Problem Message-Id: <-37786-080923081506-4715-8PT+BPRNHDBhRLgHHFbzHA::server.ccl.net> X-Original-From: "Kostas Sakellaris" Date: Tue, 23 Sep 2008 08:15:01 -0400 Sent to CCL by: "Kostas Sakellaris" [ksakell _ chem.uoa.gr] Hello! I'm a new user and this is my first question. I'm trying to perform a geometry optimization in GAUSSIAN03 on a Rhenium complex compound using as solvent acetonitrile. The geometry checkpoint that I use is that of the air-phase optimization which was successfully carried out at an earlier calculation. The gaussian input file is as follows: %Chk=re %Mem=1GB %NProc=2 #P B3LYP/LANL2DZ 5D 7F POP=REGULAR GFPRINT GFINPUT IOp(6/7=3) IOp(1/19=7) SCRF=(CPCM, Solvent=Acetonitrile,) SCF(MaxCyc=250,Conver=6) Geom=Checkpoint Guess=Read Opt=gdiis TEST Re complex 0,1 TSNUM=100 RADII=UAKS The problem is that instead of getting lower energy levels after each iteration the energy goes up! I'd greatly appreciate any suggestions since I'm new in DFT calculations and I've been trying to cope with this problem for more than 3 weeks. Thank you in advance Kostas Sakellaris ksakell^^chem.uoa.gr From owner-chemistry@ccl.net Tue Sep 23 14:51:01 2008 From: "Ol Ga eurisco1*o*pochta.ru" To: CCL Subject: CCL:G: Gaussian Solvent Optimization Problem Message-Id: <-37787-080923142318-21101-6sf86EDJXnJ6JI0ARq/now(_)server.ccl.net> X-Original-From: "Ol Ga" Date: Tue, 23 Sep 2008 14:23:14 -0400 Sent to CCL by: "Ol Ga" [eurisco1 a pochta.ru] Dear Kostas Sakellaris, Your input file is wrong. I mean your syntax and idea. I suggest you to use IOP with caution. I suggest you to use IOP if you know what you do. You made an error you typed IOp(1/19=7). Your definition of ECP is not very right. Yes, it works. But there is other style in Gaussian manual. And the whole my practice got me evidences that long description is the best choice. Please, see the corrected by me input file below. I hope it works (I checked on other Re - compound ) :-) Sincerely, Ol Ga %Chk=re %Mem=1GB %NProc=2 #P B3LYP/lanl2dz 5D 7F NoSymm POP=REGULAR GFPRINT GFINPUT IOp(6/7=3) # SCRF=(CPCM, Solvent=Acetonitrile,read) # SCF(MaxCyc=250,Conver=6) Geom=Checkpoint Guess=Read Opt=gdiis Re complex 0,1 -Re, element_1, element_2, , element_N 0 Lanl2dz **** !here is a description of ECP by definition of GAUSSIAN manual -Re 0 Lanl2dz ! CPCM, Solvent=Acetonitrile TSNUM=100 RADII=UAKS > Sent to CCL by: "Kostas Sakellaris" [ksakell _ chem.uoa.gr] > Hello! I'm a new user and this is my first question. > I'm trying to perform a geometry optimization in GAUSSIAN03 on a > Rhenium complex compound using as solvent acetonitrile. The geometry > checkpoint that I use is that of the air-phase optimization which > was successfully carried out at an earlier calculation. The gaussian input file is as follows: > %Chk=re > %Mem=1GB > %NProc=2 > #P B3LYP/LANL2DZ 5D 7F > POP=REGULAR GFPRINT GFINPUT IOp(6/7=3) IOp(1/19=7) > SCRF=(CPCM, Solvent=Acetonitrile,) > SCF(MaxCyc=250,Conver=6) Geom=Checkpoint Guess=Read Opt=gdiis TEST > > Re complex > > 0,1 > > TSNUM=100 > RADII=UAKS > The problem is that instead of getting lower energy levels after > each iteration the energy goes up! > I'd greatly appreciate any suggestions since I'm new in DFT > calculations and I've been trying to cope with this problem for more than 3 weeks. > Thank you in advance > Kostas Sakellaris > ksakell- -chem.uoa.gr From owner-chemistry@ccl.net Tue Sep 23 15:26:00 2008 From: "Ol Ga eurisco1..pochta.ru" To: CCL Subject: CCL: SUMMARY: Program for INDO/S calculations Message-Id: <-37788-080923151206-1178-+jwElLoNYQL+a3XGZlINCw-.-server.ccl.net> X-Original-From: "Ol Ga" Date: Tue, 23 Sep 2008 15:12:03 -0400 Sent to CCL by: "Ol Ga" [eurisco1%pochta.ru] Dear Gustavo L.C. Moura, I think that it is necessary to add in your summary the program ORCA. I sent this answer after your SUMMARY because I am not a specialist in semi-empirical calculations. But I think that you need to pay special attention on the program ORCA. For instance, I found out in ORCA-manual on page 271 the test job # ----------------------- # ORCA Test # ----------------------- # # Test CIS in conjunction with INDO/S # ! RHF ZINDO/S TightSCF DIIS NoRICO NoMOPrint %cis NRoots 40 MaxDim 160 end * xyz 0 1 Fe -0.01736 0.71832 -0.30714 C 2.65779 4.03195 -0.13175 C 3.51572 3.02488 -0.24101 C 2.66971 1.82027 -0.30891 C 3.30062 0.51609 -0.42755 C 2.61022 -0.60434 -0.47131 C 3.32146 -1.89491 -0.57434 C 2.35504 -2.79836 -0.57179 Etc. I hope that the ORCA test job which was cited above gets you necessary useful information about calculation. And once again I am not a specialist in semi-empirical calcs. I suggest you to have a look on ORCA (free (!) for academic use) and ORCA-manual. Sincerely, Ol Ga > Sent to CCL by: "Gustavo L.C. Moura" [gustavo**mercury.chem.pitt.edu] > Dear CCL Readers, > last week I sent a message to the list inquiring about a > program for performing INDO/S calculations with certain specifications. > I have received three suggestions of codes that I am quoting below: > 1-Jeff Reimers' (at U. Sydney, Australia) CNDO code which also does > INDO/S (http://www.chem.usyd.edu.au/~reimers/); > 2-David Yaron (at Carnegie Mellon) has his own INDO/S code; > 3-Christopher Cramer has a code called ZINDO-MN for such calculations. > Thank you for all the suggestions I have received. > Sincerely yours, > Dr. Gustavo L.C. Moura > gustavo /at/ mercury.chem.pitt.edu > ORIGINAL MESSAGE: > Dear CCL Readers, > I am looking for a program that performs INDO/S calculations and > has the following specifications: > 1- the program should be able to handle very large excitation windows > in the CIS calculations. I have met serious problems with the program I > am using right now. When I try to run calculations with large numbers > of occupied/unoccupied orbitals the program simply refuses to perform > the calculations. > 2- the program should print the dipole moments of the excited states > and the transition dipole moments between excited states. I want to > calculate the nonlinear optical properties of organic molecules and I > need these dipole moments in my calculations. > Thank you very much in advance for your answers to my question. > Sincerely yours, > Dr. Gustavo L.C. Moura > gustavo /at/ mercury.chem.pitt.edu From owner-chemistry@ccl.net Tue Sep 23 16:05:01 2008 From: "Rick Venable venabler/a\nhlbi.nih.gov" To: CCL Subject: CCL: Heme parameters Message-Id: <-37789-080923141804-20685-beJZc+Pasg1+Vp2shwhUaQ#%#server.ccl.net> X-Original-From: Rick Venable Content-transfer-encoding: 7bit Content-type: text/plain; charset="US-ASCII" Date: Tue, 23 Sep 2008 13:42:57 -0400 Mime-version: 1.0 Sent to CCL by: Rick Venable [venabler-$-nhlbi.nih.gov] In a similar way, the academic CHARMM parameters are freely available "as is" at http://mackerell.umaryland.edu/CHARMM_ff_params.html It should be noted that these parameters are developed for use with the CHARMM program; in general, developers and maintainers of other programs which use them are responsible for using these files correctly, and for keeping their programs up to date wrt. to new features. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 9/22/08 7:34 AM, "David A. Case case#,#biomaps.rutgers.edu" wrote: > > Sent to CCL by: "David A. Case" [case~!~biomaps.rutgers.edu] > > On Mon, Sep 22, 2008, Markus Kaukonen markus.kaukonen*o*iki.fi wrote: >> >> >> There are old heme parameters for in amber and you can perhaps convert >> to gromacs. >> Unfortunately Amber costs money (I guess the same goes for Charmm). > > Just a note: the AmberTools package, which contains all our preparation > and analysis tools, as well as codes for nonperiodic simulations, is > available without cost (under the GPL license). See > http://ambermd.org/#AmberTools. > > In particular, AmberTools contains the older heme parameters and codes > to incorporate them into proteins. Unfortunately, we do not have more > up-to-date heme parameters. > > ...dave case > From owner-chemistry@ccl.net Tue Sep 23 16:36:01 2008 From: "Ol Ga eurisco1~!~pochta.ru" To: CCL Subject: CCL:G: Gaussian Solvent Optimization Problem Message-Id: <-37790-080923155818-30226-3m8AiSjCiSy584UCtvCixg===server.ccl.net> X-Original-From: "Ol Ga" Date: Tue, 23 Sep 2008 15:58:14 -0400 Sent to CCL by: "Ol Ga" [eurisco1]=[pochta.ru] Dear Kostas Sakellaris, I made a huge MISPRINT when I prepared corrected version of route card to solve your problem. I am apologizing for my error. The input section SHOULD BE %Chk=re %Mem=1GB %NProc=2 #P B3LYP/GEN PSEUDO=READ 5D 7F NoSymm POP=REGULAR GFPRINT GFINPUT # IOp(6/7=3) Geom=Checkpoint Guess=Read Opt=gdiis # SCRF=(CPCM, Solvent=Acetonitrile,read) # SCF(MaxCyc=250,Conver=6) Re complex 0,1 -Re, element_1, element_2, , element_N 0 Lanl2dz **** !here is a description of ECP by definition of GAUSSIAN manual -Re 0 Lanl2dz ! CPCM, Solvent=Acetonitrile TSNUM=100 RADII=UAKS Sorry again. Sincerely, Ol Ga From owner-chemistry@ccl.net Tue Sep 23 17:14:00 2008 From: "John Merle jkmerle||yahoo.com" To: CCL Subject: CCL:G: HR problem with G03: Problem with the number of degrees of freedom Message-Id: <-37791-080923164546-1077-7O3wSFnkpEl1TK1t9Bau2A#server.ccl.net> X-Original-From: John Merle Content-Type: text/plain; charset=us-ascii Date: Tue, 23 Sep 2008 12:45:28 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: John Merle [jkmerle]_[yahoo.com] Yangsoo, I have done some work in this area and my general impression regarding thermal corrections due to hindered rotors is not a simple problem and when molecules have many degrees of freedom (e.g., long chain alkanes) the problem is very complex. In my experience Gaussian has a difficult time identifying hindered rotor in all but the simplest cases (e.g., 1 methyl group). The best way to identify them is manually. Then you can calculate the potential surface of the bond rotation to confirm whether or not you should treat it as a hindered rotor. Once identified you can use the Pitzer / Gwynn tables to determine the correction. Several groups also determine the corrections theoretically. I know Joe Bozzelli at the New Jersey Institute of Tech. does this a lot. I remember using some code from John Barker's (U. Mich.) Multiwell program as well. John Merle --- On Tue, 9/23/08, Yangsoo Kim vsmember*_*gmail.com wrote: > From: Yangsoo Kim vsmember*_*gmail.com > Subject: CCL:G: HR problem with G03: Problem with the number of degrees of freedom > To: "Merle, John K " > Date: Tuesday, September 23, 2008, 4:40 AM > Sent to CCL by: "Yangsoo Kim" > [vsmember:+:gmail.com] > Dear All, > > A while ago, I posted a problem on hindered rotor > calculation with G03, > which is the one that other users also have. The related > CCL posts on the > problems are attached below. Basically, G03 terminated with > the error > message "Problem with the number of degrees of > freedom", when molecules > other than alkane are calculated for hindered rotor > analysis. > > I wonder if there is any clue that has been posted or > found. I would greatly > appreciate if any one of you provides any clue to solve > this problem. > > If this is under correction for now and there is no > solution at this time > > from G03 side, is there any other program that I can > use for automatic HR > identification and calculation for thermo property > estimation? > > Many thanks in advance, > > Yangsoo Kim > > > ================================================================ > CCL:G: Hinderedrotor Problem in Gaussian03 > .. From: "Greef, T.F.A. de" > > .. Subject: CCL:G: Hinderedrotor Problem in Gaussian03 > .. Date: Tue, 6 Nov 2007 11:10:50 +0100 > > From: owner-chemistry(!)ccl.net > [mailto:owner-chemistry(!)ccl.net] > Sent: Tuesday, November 06, 2007 9:51 AM > To: Greef, T.F.A. de > Subject: CCL:G: Hinderedrotor Problem in Gaussian03 > Dear CCL members, > I am trying to use the "HF/6-31G* opt > freq=hinderedrotor" keyword in > Gaussian03 to correct the themochemical data for > contributions of internal > rotation. > It is normally terminated to calculate the hindered rotor > analysis for the > normal alkyl-chained systems. > But I met the following error messages for various > alkyl-substitutied > benzene ring systems. (e.q. toluene, ethylbenzene or > propylbenzene) > === Error Message (propylbenzene) === > Hindered Internal Rotation Analysis > Internal coordinate list checked > Check for planar centers > 1 2 3 10 360.000 > 2 1 6 7 359.984 > 3 1 4 11 360.000 > 4 3 5 12 360.000 > 5 4 6 13 360.000 > 6 2 5 14 360.000 > Check reduced barrier height. Cut-off : V/RT = 33.7561 > Check for ring deformation > Number of internal rotation degrees of freedom = 3 > NNew= 48 NTest= 3 NB= 9 IFrz= 0 IBar= 0 > ICyc= 0 > Problem with the number of degrees of freedom > Error termination... > ====================== > Does anyone have any suggestions to solve these problems? > And please tell me another softwares to calculate the > hindered rotor. > Thanks in advance. > Yangsoo Kim > ----------------------------------------------------------------------- > CCL:G: g03 Problem with "HinderedRotor" > calculations > ________________________________________ > .. From: Ulrich Scharfenort > > .. Subject: CCL:G: g03 Problem with > "HinderedRotor" calculations > .. Date: Fri, 07 Mar 2008 11:22:51 +0100 > ________________________________________ > Sent to CCL by: Ulrich Scharfenort > [scharfenort=ltt.rwth-aachen.de] > Hello, > I hope maybe one of you can help me with an problem. > > Currently i try to calculate Aromatic compounds with the > HinderedRotor > option. With Alkanes HR works very fine and without any > problem so I think > it's not an problem with the coordinates. > The error-message is as follows: > Number of internal rotation degrees of freedom = 4 > NNew= 30 NTest= 4 NB= 10 IFrz= 0 IBar= 0 > ICyc= 0 > Problem with the number of degrees of freedom > > Error termination via Lnk1e in > /opt/GAUSSIAN/LINUX_amd64/g03.d02/l716.exe at > Fri Mar 7 11:10:19 2008. > Job cpu time: 0 days 0 hours 0 minutes 15.4 seconds. > > File lengths (MBytes): RWF= 17 Int= 0 D2E= 0 Chk= 10 Scr= 1 > > This was a calculation for Butylbenzene where are internal > rotations. > Does HR only work for Alkanes and nothing else? > > Maybe somebody does know for which compound classes HR > works and for which > not or and way to make it working for all compounds. > I will appreciate all the help you can provide on this > problem. > Yours sincerely > > ; > Ulrich Scharfenort > > ---------------------------------------------------------------------- > CCL:G: Hindered Rotor Gaussian03 > ________________________________________ > .. From: "Tom F.A. de Greef" > > .. Subject: CCL:G: Hindered Rotor Gaussian03 > .. Date: Thu, 18 Jan 2007 04:38:20 -0500 > ________________________________________ > Sent to CCL by: "Tom F.A. de Greef" > [t.f.a.d.greef ~ tue.nl] > Dear all, > I want to report some deltaG values generated by a > Gaussian03 job on a > molecule > of about 20 heavy atoms (B3LYP,6_311G+(d,p). However, I > want to check if > the > assumptian that Gaussian03 makes are correct (the free > rotor assumption). I > requested a fequency job using the optimised geometry at > the > before mentioned level using these keywords: > freq=hindered rb3lyp/6-311+g(d,p) > geom=(connectivity,modredundant) > "Geometry in Cartesian coordinates" > It computes all the derivatives and computes the full > mass-weighted force > constant matrix. The calculation then starts a hindered > rotation analysis: > Internal coordinate list checked > Check for planar centers > 1 2 4 27 359.993 > 2 1 9 28 359.996 > 3 4 5 8 359.927 > 4 1 3 29 359.965 > 5 3 6 15 360.000 > 7 8 11 12 359.998 > 8 3 7 9 360.000 > 9 2 8 10 359.998 > 10 9 11 13 360.000 > 11 7 10 14 359.994 > 15 5 18 21 359.928 > 16 17 20 33 359.996 > 17 16 18 34 359.993 > 18 15 17 35 359.965 > 19 20 23 25 360.000 > 20 16 19 21 359.998 > 21 15 20 22 360.000 > 22 21 23 24 359.999 > 23 19 22 26 359.993 > Check reduced barrier height. Cut-off : V/RT = 33.7561 > Bond 3 - 5 frozen. > Estimated reduced barrier height : V/RT = > 37.5137 For a > periodicity of : 2 > Bond 5 - 15 frozen. > Estimated reduced barrier height : V/RT = > 37.5712 For a > periodicity of : 2 > Check for ring deformation > Number of internal rotation degrees of freedom = 2 > NNew= 92 NTest= 2 NB= 24 IFrz= 0 IBar= 2 > ICyc= 0 > Problem with the number of degrees of freedom > Error termination via Lnk1e in > /usr/opt/gaussian/g03/l716.exe > I know that the method used by Gaussian03 to correct for > hindered rotation > is > not always working (for example it works for butane but > fails for > methanol). For > underlying thheory: P.Y. Ayala & H.B. Schlegel, JCP > 108,2314 > Best regards, > Tom de Greef > ------------------------------------------------------------------ > CCL:G: Guassian - Hindered rotor frequency option > ________________________________________ > .. From: "Rob Noble-Eddy" > > .. Subject: CCL:G: Guassian - Hindered rotor frequency > option > .. Date: Fri, 9 Nov 2007 09:34:04 -0500 > ________________________________________ > Sent to CCL by: "Rob Noble-Eddy" > [r.noble-eddy^-^ed.ac.uk] > Hi, > I have a molecule which contains a phenyl group, and want > to calculate the > free > energies of its two conformers. The barrier to rotation of > the phenyl group > is > around kT and so I believe any estimation of the free > energy should include > this > rotation, rather than simply using a standard frequency > calculation on the > equilibrium position. > I tried to use the freq=hinderedrotor option in gaussian > '03 to achieve > this, > but after successfully completing a geometry optimisation > it starts to do > the > frequency calculation, but stops with an error when it > tries to determine > if > there are any hindered rotors in the molecule. > I've included the output below, if anyone has any > ideas, or has used this > feature before please get in touch. > Thanks, > Rob > ============================================ > Internal coordinate list checked > Check for planar centers > 1 2 3 7 359.997 > 2 1 4 9 360.000 > 3 1 5 10 360.000 > 4 2 6 11 360.000 > 5 3 6 12 360.000 > 6 4 5 13 360.000 > Check reduced barrier height. Cut-off : V/RT = 33.7561 > Check for ring deformation > Number of internal rotation degrees of freedom = 2 > NNew= 36 NTest= 2 NB= 8 IFrz= 0 IBar= 0 > ICyc= 0 > Problem with the number of degrees of freedom > Error termination via Lnk1e in > /usr/local/Chem-Apps/g03_d01/g03/l716.exe > at Fri > Nov 9 11:29:03 2007. > > ------------------------------------------------------------ > CCL:G: How to Identify and correct for Hindered Rotors in > G03 > ________________________________________ > .. From: akef afaneh > .. Subject: CCL:G: How to Identify and correct for Hindered > Rotors in > G03 > .. Date: Fri, 23 Nov 2007 06:37:39 -0800 (PST) > ________________________________________ > Sabry; > I do not know if I can help you to solve your problem or > not. However, I > need more information about your job to give you a suitable > example. What I > see here from the output massage is that the problem in the > constrained mode > # 2, so, the program gave you a message to redo the normal > mode analysis > with added constraints. You have also a problem in the > number of degrees of > freedom, these usually result when a certain degree of > symmetry is used and > the Gaussian recognizes another symmetry. > When we study a TS species with unrecognized bond, > Geom=Modify keyword is > usually used. > > Akef > > -------------------------------------------------------------------- > Hello CCLers, > > I'm trying to correct for hindered rotation modes using > the keyword > Freq=HinderedRotor in G03. > In fact I have no idea how to do that; I mean the > identification and the > correction. For the reactant the job terminated > successfully > but I don't know what I should get from the output. > Fot the TS, the job > failed with the following error message: > ---------------------------------------------------------------------------- > ----- > Check correspondance between vibrational and internal > rotation modes > frequencies in cm**-1 > 1 2 3 > Frequencies --- 95.0468 155.4019 177.3364 > -1474.4902 0.0101 0.0562 -0.0333 > 92.0838 -0.9973 0.4231 0.6332 > 136.3765 -0.2606 0.8307 0.3015 > 155.3244 0.4631 -0.8491 -0.9191 > 195.3921 -0.6826 0.4576 0.8660 > 343.8586 - 0.8442 0.7230 0.8824 > > ---------------------------------------------------------------------------- > One-to-one correspondance not acheived > Constrained mode 2 likely source of the problem > Bond # Atoms > 1 1 2 0.00000 > 2 2 3 0.07105 > 3 3 8 0.12548 > 4 8 9 0.74224 > Freeze coordinate 27 > Freeze coordinate 28 > Freeze coordinate 29 > Freeze coordinate 30 > Redo normal mode analysis with added constraints > Number of internal rotation degrees of freedom = 3 > NNew= 7 NTest= 3 NB= 4 IFrz= 1 IBar= 1 > ICyc= 0 > Problem with the number of degrees of freedom > Error termination via Lnk1e in C:\G03W\l716.exe at > Sat Nov 10 22:37:32 > 2007. > > ---------------------------------------------------------------------------- > ---------------------------------------------------- > > I don't understand what the message means. I shall be > very grateful if > anyone can help me (using a simple example would be fine) > Thank you in advance. > > Sabry Ahmed > > > -- > Sabry El-Taher Ahmed > Cairo University > Faculty of Science > Department of Chemistry > Cairo, Egypt. > > --------------------------------------------------------------- > > Hindered Rotor Analysis in G03 > ________________________________________ > .. From: Matthias Lein > > .. Subject: Hindered Rotor Analysis in G03 > .. Date: Mon, 28 Jun 2004 11:17:34 +0200 > ________________________________________ > Hi all, > investigating a molecule of 72 atoms I calculated the > thermodynamical > data of dissociation given by standard frequency analysis > of Gaussian98 > (and G03). > Given one rotational barrier of about 10 kcal/mol I > thought it to be > useful to try the "Freq(HinderedRotor)"-Keyword > in Gaussian to correct > the data for contributions of internal rotation. I used an > already > finished harmonic frequency analysis and the > "readfc"-keyword to avoid > recalculation of the frequencies. > The algorithm of Schlegel et al. found two internal > rotations but then > skipped the calculation with the following lines: > > Check for ring deformation > > Number of internal rotation degrees of freedom = 2 > > NNew= 156 NTest= 2 NB= 45 IFrz= 0 IBar= 7 > ICyc= 0 > > Problem with the number of degrees of freedom > > Error termination via Link716 > My questions: > 1) Does anyone know the limitations of this keyword? (No > of atoms, > degrees of freedom,...) > 2) Is there knowledge about problems and performance of > this method, > including numerical values (is it necessary or reasonable > to use these > corrections)? > Thanks in advance > Matthias. > > > > -= This is automatically added to each message by the > mailing script =- > To 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> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search) From owner-chemistry@ccl.net Tue Sep 23 17:48:00 2008 From: "Vincenzo Verdolino vincenzo.verdolino..nemo.unipr.it" To: CCL Subject: CCL:G: Gaussian Solvent Optimization Problem Message-Id: <-37792-080923123934-10764-rlFVhj5HFNWX/QapXKUYuA-x-server.ccl.net> X-Original-From: "Vincenzo Verdolino" Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 23 Sep 2008 16:35:20 +0200 MIME-Version: 1.0 Sent to CCL by: "Vincenzo Verdolino" [vincenzo.verdolino#%#nemo.unipr.it] Hi I can suggest you some hint. Firstly, if you don't have particular reasons, you can try ti use scrf=iefpcm instead of cpcm. Then I suggest to use radii=ua0 or uff (but anyway uaks is not a bad choice at the dft level, but watch out if you are going to performe an HF calculation. In this case you will use UAHF) It could be possible that the optimization will be "unstable" close to the Threshold. Don't worry about this, you can try to turn off the added spheres with noaddsph (look into the gaussian.com page under the scrf keyword). Finally you can also try with tsare=0.3 (default) or tsare=0.4 Good luck Vincenzo On Tue, 23 Sep 2008 08:15:01 -0400, Kostas Sakellaris ksakell,+,chem.uoa.gr wrote > Sent to CCL by: "Kostas Sakellaris" [ksakell _ chem.uoa.gr] > Hello! I'm a new user and this is my first question. > > I'm trying to perform a geometry optimization in GAUSSIAN03 on a > Rhenium complex compound using as solvent acetonitrile. The geometry > checkpoint that I use is that of the air-phase optimization which > was successfully carried out at an earlier calculation. The gaussian > input file is as follows: > > %Chk=re > %Mem=1GB > %NProc=2 > #P B3LYP/LANL2DZ 5D 7F > POP=REGULAR GFPRINT GFINPUT IOp(6/7=3) IOp(1/19=7) > SCRF=(CPCM, Solvent=Acetonitrile,) > SCF(MaxCyc=250,Conver=6) Geom=Checkpoint Guess=Read Opt=gdiis TEST > > Re complex > > 0,1 > > TSNUM=100 > RADII=UAKS > > The problem is that instead of getting lower energy levels after > each iteration the energy goes up! > > I'd greatly appreciate any suggestions since I'm new in DFT > calculations and I've been trying to cope with this problem for more > than 3 weeks. Thank you in advance > > Kostas Sakellaris > > ksakell- -chem.uoa.gr > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the [A] sign. You can > also> > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)-- Universita' degli Studi di Parma (http://www.unipr.it) From owner-chemistry@ccl.net Tue Sep 23 18:56:00 2008 From: "gustavo,+,mercury.chem.pitt.edu" To: CCL Subject: CCL: SUMMARY: Program for INDO/S calculations Message-Id: <-37793-080923175629-4084-fA+22vO2sbYOEdAewBZhOw++server.ccl.net> X-Original-From: gustavo,mercury.chem.pitt.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 23 Sep 2008 16:41:24 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: gustavo:+:mercury.chem.pitt.edu Dear Ol Ga, I had already considered ORCA, contacted Frank Neese and received the following answer. >> First I would like to know if ORCA can handle large excitations >> windows in the CIScalculations. >> >yes, it is AO integral direct and can, in principle, easily do (almost) >arbitrarily large molecules in very short time. > >> Second I would like to know if ORCA prints the dipole moments of the >> excited states and the transition dipole moments >> >> between excited states. >> >no, orca does at least presently not do that. Maybe we put it in at >some point. Therefore, ORCA does not work for me, yet. Thanks for you reply. Sincerely yours, Gustavo L.C. Moura > > Sent to CCL by: "Ol Ga" [eurisco1%pochta.ru] > Dear Gustavo L.C. Moura, > > > I think that it is necessary to add in your summary the program ORCA. I > sent this answer after your SUMMARY because I am not a specialist in > semi-empirical calculations. But I think that you need to pay special > attention on the program ORCA. For instance, I found out in ORCA-manual on > page 271 the test job > > # ----------------------- > # ORCA Test > # ----------------------- > # > # Test CIS in conjunction with INDO/S > # > ! RHF ZINDO/S TightSCF DIIS NoRICO NoMOPrint > %cis NRoots 40 > MaxDim 160 > end > * xyz 0 1 > Fe -0.01736 0.71832 -0.30714 > C 2.65779 4.03195 -0.13175 > C 3.51572 3.02488 -0.24101 > C 2.66971 1.82027 -0.30891 > C 3.30062 0.51609 -0.42755 > C 2.61022 -0.60434 -0.47131 > C 3.32146 -1.89491 -0.57434 > C 2.35504 -2.79836 -0.57179 > > Etc. > > I hope that the ORCA test job which was cited above gets you necessary > useful information about calculation. And once again I am not a specialist > in semi-empirical calcs. I suggest you to have a look on ORCA (free (!) > for academic use) and ORCA-manual. > > Sincerely, > > Ol Ga > > > > >> Sent to CCL by: "Gustavo L.C. Moura" [gustavo**mercury.chem.pitt.edu] >> Dear CCL Readers, >> last week I sent a message to the list inquiring about a >> program for performing INDO/S calculations with certain specifications. >> I have received three suggestions of codes that I am quoting >> below: > >> 1-Jeff Reimers' (at U. Sydney, Australia) CNDO code which also >> does >> INDO/S (http://www.chem.usyd.edu.au/~reimers/); >> 2-David Yaron (at Carnegie Mellon) has his own INDO/S code; >> 3-Christopher Cramer has a code called ZINDO-MN for such >> calculations. > >> Thank you for all the suggestions I have received. >> Sincerely yours, >> Dr. Gustavo L.C. Moura >> gustavo /at/ mercury.chem.pitt.edu > > >> ORIGINAL MESSAGE: > > >> Dear CCL Readers, >> I am looking for a program that performs INDO/S calculations and >> has the following specifications: >> 1- the program should be able to handle very large excitation windows >> in the CIS calculations. I have met serious problems with the program I >> am using right now. When I try to run calculations with large numbers >> of occupied/unoccupied orbitals the program simply refuses to perform >> the calculations. >> 2- the program should print the dipole moments of the excited states >> and the transition dipole moments between excited states. I want to >> calculate the nonlinear optical properties of organic molecules and I >> need these dipole moments in my calculations. >> Thank you very much in advance for your answers to my question. >> Sincerely yours, >> Dr. Gustavo L.C. Moura >> gustavo /at/ mercury.chem.pitt.edu> > > From owner-chemistry@ccl.net Tue Sep 23 22:57:01 2008 From: "Geoffrey Hutchison geoffh*pitt.edu" To: CCL Subject: CCL: Inverse Molecular Design Methods Message-Id: <-37794-080923192830-21767-KIYAiFSYX5rENmgoOce9jA:+:server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Tue, 23 Sep 2008 18:49:36 -0400 Mime-Version: 1.0 (Apple Message framework v929.2) Sent to CCL by: Geoffrey Hutchison [geoffh * pitt.edu] I'm currently writing a paper which involves "inverse design" -- new molecular structures which are optimal solutions for a particular property. I'm aware of a number of attempts in this area, including data mining, "inverse QSAR," combinatorial libraries, and some types of genetic algorithms. What I'm interested is some of the new "alchemical" QM methods, like Weitao Yang and David Beratan at Duke. These methods can refine molecular structures by changing atomic composition. I remember hearing about a few other such methods, but can't seem to find them now via Google, Web of Science, etc. I'll be happy to summarize articles/references to the list afterwards. Thanks very much! -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry, University of Pittsburgh 219 Parkman Avenue, Pittsburgh, PA 15260 http://hutchison.chem.pitt.edu/ (412) 648-0492