From owner-chemistry@ccl.net Tue Jan 22 05:42:01 2008 From: "Mark Mackey mark*o*cresset-bmd.com" To: CCL Subject: CCL: G03 compilation: compilers? Message-Id: <-36082-080122050317-26148-X2svAH0W6FU6r2ASotQkdw,server.ccl.net> X-Original-From: Mark Mackey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 22 Jan 2008 09:28:45 +0000 MIME-Version: 1.0 Sent to CCL by: Mark Mackey [mark[A]cresset-bmd.com] Michael Krein kreinm2{:}rpi.edu wrote: > > While it may be possible, I would strongly recommend against using > IFORT/ICC with anything not Intel... IFORT/ICC builds runtime checks > into every executable... if it's found that your machine isn't > GenuineIntel, well, you're executing the i386 non-optimized codepath, > if you can execute at all. > This isn't true in 64-bit: the Intel compilers 'base' hardware support is for P4/SSE2 in 64-bit mode. In 32-bit mode you are correct: non-Intel chips can end up running non-vectorised code depending on your compilation options. However, it is easy to patch the compiler and/or the executables to remove this check: see http://www.swallowtail.org/naughty-intel.html for details and a simple script to do the patch. Mark. -- Dr Mark Mackey Cresset BioMolecular Discovery Ltd From owner-chemistry@ccl.net Tue Jan 22 07:13:00 2008 From: "Jamie Platts platts[]Cardiff.ac.uk" To: CCL Subject: CCL: MGMS Spring meeting 2008 Message-Id: <-36083-080122071056-9637-3FGNnPUlwe5pwOlFssdnsQ^-^server.ccl.net> X-Original-From: "Jamie Platts" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Tue, 22 Jan 2008 11:24:25 +0000 Mime-Version: 1.0 Sent to CCL by: "Jamie Platts" [platts-x-Cardiff.ac.uk] Dear CCL Registration is open now for the Molecular Graphics and Modelling Society's Spring meeting on Computational Bio-Inorganic Chemistry, which will be held in Cardiff from 31st March to 1st April 2008. Early registration fees will apply for a few more weeks, closing on 8th Feb. Thanks to generous sponsorship by CCG, travel bursaries for students and younger researchers will be available. We have an excellent line-up of speakers, all of whom have recently confirmed their attendance: * Dr. Frank Blaney - Cytochrome P450 2D6 - Recent Structural and Mechanistic Studies. * Prof. Jaroslav Burda - Physicochemical properties and reaction mechanisms of selected anticancer metallodrugs. * Prof. Paolo Carloni - Metal-based drugs/DNA interactions investigated by molecular simulation * Dr. Rob Deeth - Bridging Ligands at Multinuclear Metalloenzyme Active Sites: Novel Force Field Approaches for Dimanganese(II) and Dicopper(II) Systems * Dr. Jeremy Harvey - QM/MM Studies of Metalloprotein Structure and Reactivity * Prof. Fahmi Himo - On the Elusive Mechanism of Nitrile Hydratase * Prof. Nigel Richards - Fe-type nitrile hydratase: How does sulfur oxidation modulate metal chemistry? * Dr. Sam de Visser - Catalytic properties of oxygen activating non-heme enzymes In addition, Dr. Nick Besley will present the MGMS Silver Jubilee Prize lecture, titled: State-Selective Self-Consistent Field Calculations using the Maximum Overlap Method. More details on the meeting, including registration and accomodation details, can be found at URL: http://theory.chem.cf.ac.uk/~grant/conf We look forward to seeing you in Cardiff soon! Jamie ---------------------------------------------------------- Jamie Platts School of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts|,|cf.ac.uk Park Place FAX: +44 (0) 2920 874030 Cardiff CF10 3AT www.cf.ac.uk/chemy From owner-chemistry@ccl.net Tue Jan 22 09:06:00 2008 From: "Hadley Clayton clayths^unisa.ac.za" To: CCL Subject: CCL:G: Gaussian 03 Memory Message-Id: <-36084-080122043728-22561-Aiu6IRbELAkuJ+RLU1Gbfw*o*server.ccl.net> X-Original-From: "Hadley Clayton" Date: Tue, 22 Jan 2008 04:37:23 -0500 Sent to CCL by: "Hadley Clayton" [clayths||unisa.ac.za] I'm running Gaussian 03 on 8 node cluster using only approx 1% of memory yet get the following message when submitting a job (see output below). Can anyone tell me how to correct this problem. Thanks. ********************************************** Gaussian 03: x86-Linux-G03RevB.05 24-Oct-2003 22-Jan-2008 ********************************************** %chk=FpCl_test1.chk %mem=16MW %nproc=1 Will use up to 1 processors via shared memory. Erroneous write during file extend. write 2624 instead of 4096 Probably out of disk space. error in NtrExt1 From owner-chemistry@ccl.net Tue Jan 22 10:28:00 2008 From: "Michael Krein kreinm2]~[rpi.edu" To: CCL Subject: CCL:G: Gaussian 03 Memory Message-Id: <-36085-080122102645-10319-g9sKEnK9uqFRADQRa4d2bg _ server.ccl.net> X-Original-From: Michael Krein Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Tue, 22 Jan 2008 10:26:26 -0500 Mime-Version: 1.0 (Apple Message framework v915) Sent to CCL by: Michael Krein [kreinm2**rpi.edu] Are you by any chance running Red Hat 5 / Centos 5? I've run into this problem before, and a solution provided at http://www.linuxquestions.org/questions/linux-software-2/how-do-i-get-gaussian-03-a-quantum-chemical-program-to-work-on-fedora-core-5-455395/ seems to work for me... The linux command that I've added to my /etc/profile is echo 0 > /proc/sys/kernel/randomize_va_space Does this work for you as well? Cheers, -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- Michael Krein Breneman Research Group Rensselaer Exploratory Center for Cheminformatics Research Rensselaer Polytechnic Institute -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- On Jan 22, 2008, at 4:37 AM, Hadley Clayton clayths^unisa.ac.za wrote: > > Sent to CCL by: "Hadley Clayton" [clayths||unisa.ac.za] > > I'm running Gaussian 03 on 8 node cluster using only approx 1% of > memory yet get the following message when submitting a job (see > output below). Can anyone tell me how to correct this problem. Thanks. > > ********************************************** > Gaussian 03: x86-Linux-G03RevB.05 24-Oct-2003 > 22-Jan-2008 > ********************************************** > > %chk=FpCl_test1.chk > %mem=16MW > %nproc=1 > > Will use up to 1 processors via shared memory. > Erroneous write during file extend. write 2624 instead of > 4096 > Probably out of disk space. > error in NtrExt1 > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > From owner-chemistry@ccl.net Tue Jan 22 11:02:00 2008 From: "Hemant Srivastava hemantkrsri-#-gmail.com" To: CCL Subject: CCL:G: Gaussian 03 Memory Message-Id: <-36086-080122104139-17165-Nf7/pSDarmhUDSuEnDy/OQ ~~ server.ccl.net> X-Original-From: "Hemant Srivastava" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 22 Jan 2008 16:37:33 +0200 MIME-Version: 1.0 Sent to CCL by: "Hemant Srivastava" [hemantkrsri|*|gmail.com] Hi, If you have enough disk space I think you need to increase memory. try %mem=50MW or more depend on the size Your system is 32 bit or 64 bit? Hope it will help =========================================================== On 1/22/08, Hadley Clayton clayths^unisa.ac.za wrote: > > Sent to CCL by: "Hadley Clayton" [clayths||unisa.ac.za] > > I'm running Gaussian 03 on 8 node cluster using only approx 1% of memory yet get the following message when submitting a job (see output below). Can anyone tell me how to correct this problem. Thanks. > > ********************************************** > Gaussian 03: x86-Linux-G03RevB.05 24-Oct-2003 > 22-Jan-2008 > ********************************************** > > %chk=FpCl_test1.chk > %mem=16MW > %nproc=1 > > Will use up to 1 processors via shared memory. > Erroneous write during file extend. write 2624 instead of > 4096 > Probably out of disk space. > error in NtrExt1> > > From owner-chemistry@ccl.net Tue Jan 22 15:09:00 2008 From: "jitrayut jitonnom jitrayut.018,gmail.com" To: CCL Subject: CCL: Potential Surface Scan Message-Id: <-36087-080122015142-5517-JU78qJ+Oc2NfKQXR8nUM1Q|*|server.ccl.net> X-Original-From: "jitrayut jitonnom" Content-Type: multipart/alternative; boundary="----=_Part_23641_32404868.1200981188186" Date: Tue, 22 Jan 2008 12:53:08 +0700 MIME-Version: 1.0 Sent to CCL by: "jitrayut jitonnom" [jitrayut.018:_:gmail.com] ------=_Part_23641_32404868.1200981188186 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear CCL community, I have problem about the output of running Potential Surface Scan in line " Summary of Optimized Potential Surface Scan"with the following input; %chk=test-BF.chk %mem=6MW %nproc=1 # hf/6-31g opt=z-matrix nosymm C 21 B22 2 A21 1 tor tor 0.0 S 13 +15.0 The output error is the Eigenvalue which is ****** what is this symbol? when i try with AM1 calculation the Eigenvalue is ok. So, is there something mistage about the method or just my mistage somewhere please check the output below. Summary of Optimized Potential Surface Scan 1 2 3 4 5 EIGENVALUES -- ************************************************** B1 1.39996 1.39889 1.39745 1.39626 1.39516 B2 1.40273 1.40203 1.40051 1.39910 1.39808 B3 1.37890 1.37911 1.37962 1.38022 1.38077 B4 1.39459 1.39530 1.39610 1.39654 1.39669 B5 1.38309 1.38363 1.38428 1.38464 1.38467 B6 1.06927 1.07052 1.07196 1.07284 1.07317 B7 1.07010 1.07150 1.07294 1.07369 1.07397 D17 -179.99458-180.01870-180.00589-179.99765-179.98866 D18 -180.00074-177.98783-178.74325-180.06775-180.97743 D19 -179.99528-161.51052-147.91222-135.19630-121.68689 tor 0.00000 15.00000 30.00000 45.00000 60.00000 Anyone who have experienced in this problem, please help me !! Best regards, Jitrayut Jitonnom ------=_Part_23641_32404868.1200981188186 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear CCL community,
 
I have problem about the output of running Potential Surface Scan in line " Summary of Optimized Potential Surface Scan"with the following input;

%chk=test-BF.chk
%mem=6MW
%nproc=1
# hf/6-31g opt=z-matrix nosymm

 C                 21             B22    2             A21    1             tor
   tor            0.0 S 13 +15.0

The output error is the Eigenvalue which is ****** what is this symbol?  when i try with AM1 calculation the Eigenvalue is ok. So, is there something mistage about the method or just my mistage somewhere please check the output below.

 Summary of Optimized Potential Surface Scan
                           1         2         3         4         5
     EIGENVALUES --  **************************************************
           B1           1.39996   1.39889   1.39745   1.39626   1.39516
           B2           1.40273   1.40203   1.40051   1.39910   1.39808
           B3           1.37890   1.37911   1.37962   1.38022   1.38077
           B4           1.39459   1.39530   1.39610   1.39654   1.39669
           B5           1.38309   1.38363   1.38428   1.38464   1.38467
           B6           1.06927   1.07052   1.07196   1.07284   1.07317
           B7           1.07010   1.07150   1.07294   1.07369   1.07397
           D17       -179.99458-180.01870-180.00589-179.99765-179.98866
           D18       -180.00074-177.98783-178.74325-180.06775-180.97743
           D19       - 179.99528-161.51052-147.91222-135.19630-121.68689
           tor          0.00000  15.00000  30.00000  45.00000  60.00000

Anyone who have experienced in this problem, please help me !!
 
Best regards,
 
Jitrayut Jitonnom
 
 
------=_Part_23641_32404868.1200981188186-- From owner-chemistry@ccl.net Tue Jan 22 19:46:00 2008 From: "Darren Simpson darren.simpson() unisa.edu.au" To: CCL Subject: CCL:G: Partial charges Message-Id: <-36088-080122194239-30464-5cY3l86rit5A2Rgsg74OWQ+*+server.ccl.net> X-Original-From: "Darren Simpson" Date: Tue, 22 Jan 2008 19:42:35 -0500 Sent to CCL by: "Darren Simpson" [darren.simpson^^^unisa.edu.au] Dear CCL members, I have optimized the structure of a PtCl6_2- anion model as described below in the GAUSSIAN03 input file. The calculation terminated normally, however the partial charges below does not seem to make sense. I was expecting the metal centre to have a positive charge, but it seems the overall negative charge was distributed evenly over all the centers. I was thinking perhaps the lanl2dz basis set is not suited to charged metal centers. Should I be using other basis sets? Any suggestions is much appreciated. With thanks, Darren Simpson, PhD Applied Centre for Structural and Synchrotron Studies University of South Australia Mawson Lakes SA 5095 Ph: +61-8-8302 5580 Fax: +61-8-8302 5545 E-mail: darren.simpson*_*unisa.edu.au Input file: # B3LYP gen opt pseudo=lanl2 scrf Pt(Cl)6 B3LYP/LANL2DZ/6-31+G(2d) Optimization -2 1 Pt 0 0. 0. 0. Cl 0 R 0. 0. Cl 0 -R 0. 0. Cl 0 0. R 0. Cl 0 0. -R 0. Cl 0 0. 0. R Cl 0 0. 0. -R R 2.315 Cl 0 6-31+g(2d) **** Pt 0 lanl2dz **** Pt 0 lanl2dz > From output file: Mulliken atomic charges: 1 1 Pt -0.394059 2 Cl -0.267657 3 Cl -0.267657 4 Cl -0.267657 5 Cl -0.267657 6 Cl -0.267657 7 Cl -0.267657 Sum of Mulliken charges= -2.00000 From owner-chemistry@ccl.net Tue Jan 22 20:43:00 2008 From: "William F. Polik polik]=[hope.edu" To: CCL Subject: CCL:G: Potential Surface Scan Message-Id: <-36089-080122195002-32602-5ntI5CsinuADGjqzj/Ti/Q{}server.ccl.net> X-Original-From: "William F. Polik" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Tue, 22 Jan 2008 17:55:21 -0500 Mime-Version: 1.0 Sent to CCL by: "William F. Polik" [polik__hope.edu] Jitrayut, We have seen this before with Gaussian. I suspect that your molecule is large enough that its computed energy is less than -1000 au. The formatting statement used to output this line is evidently limited to -999.99999, and consequently "**********" is output instead. If your are lucky, you might be able to extract the numbers from the archive section of the output (at the very end). Will Polik At 12:53 AM 1/22/2008, you wrote: >Dear CCL community, > >I have problem about the output of running Potential Surface Scan in >line " Summary of Optimized Potential Surface Scan"with the following input; > >%chk=test-BF.chk >%mem=6MW >%nproc=1 ># hf/6-31g opt=z-matrix nosymm > > C 21 B22 2 A21 1 > tor > tor 0.0 S 13 +15.0 > >The output error is the Eigenvalue which is ****** what is this >symbol? when i try with AM1 calculation the Eigenvalue is ok. So, >is there something mistage about the method or just my mistage >somewhere please check the output below. > > Summary of Optimized Potential Surface Scan > 1 2 3 4 5 > EIGENVALUES -- ************************************************** > B1 1.39996 1.39889 1.39745 1.39626 1.39516 > B2 1.40273 1.40203 1.40051 1.39910 1.39808 > B3 1.37890 1.37911 1.37962 1.38022 1.38077 > B4 1.39459 1.39530 1.39610 1.39654 1.39669 > B5 1.38309 1.38363 1.38428 1.38464 1.38467 > B6 1.06927 1.07052 1.07196 1.07284 1.07317 > B7 1.07010 1.07150 1.07294 1.07369 1.07397 > D17 -179.99458-180.01870-180.00589-179.99765-179.98866 > D18 -180.00074-177.98783-178.74325-180.06775-180.97743 > D19 - 179.99528-161.51052-147.91222-135.19630-121.68689 > tor 0.00000 15.00000 30.00000 45.00000 60.00000 >Anyone who have experienced in this problem, please help me !! > >Best regards, > >Jitrayut Jitonnom > > ================================ Dr. William F. Polik Hofma Professor of Chemistry Department of Chemistry Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik-*-hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 ================================ From owner-chemistry@ccl.net Tue Jan 22 21:18:00 2008 From: "Nuno A. G. Bandeira nuno.bandeira|*|ist.utl.pt" To: CCL Subject: CCL: Partial charges Message-Id: <-36090-080122204801-19161-/ZZR8PJ1rFaatSBWR74oTA(~)server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Date: Tue, 22 Jan 2008 20:47:58 -0500 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira a ist.utl.pt] Remember that the negative charge has to go somewhere so it's likely that you'll end up with negative charge on platinum anyway. Two things that I'd reccommend: Mulliken charges don't go well with diffuse functions so I'd remove them from the Cl atoms. Add an f function to Pt: F 1 1.0 0.993 1.0 -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student :-: IST,Lisbon --