From chemistry-request@ccl.net Mon May 19 06:19:32 2003 Received: from ns2.tudelft.nl (ns2.tudelft.nl [130.161.180.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4JAJVo8030972 for ; Mon, 19 May 2003 06:19:32 -0400 Received: from CONVERSION-DAEMON.mailhost1.tudelft.nl by mailhost1.tudelft.nl (PMDF V6.1-1 #40924) id <0HF400501Q0G4V@mailhost1.tudelft.nl> for chemistry@ccl.net; Mon, 19 May 2003 12:19:29 +0200 (MEST) Received: from mail.dct.tudelft.nl (mail.dct.tudelft.nl [130.161.196.201]) by mailhost1.tudelft.nl (PMDF V6.1-1 #40924) with ESMTP id <0HF400EM0Q0FMK@mailhost1.tudelft.nl> for chemistry@ccl.net; Mon, 19 May 2003 12:19:27 +0200 (MEST) Received: from TNW-DCT1/SpoolDir by mail.dct.tudelft.nl (Mercury 1.48); Mon, 19 May 2003 12:19:27 +0200 Received: from SpoolDir by TNW-DCT1 (Mercury 1.48); Mon, 19 May 2003 12:19:22 +0200 Date: Mon, 19 May 2003 12:19:17 +0200 From: Martijn Zwijnenburg Subject: ? in G98 output To: chemistry@ccl.net Message-id: <3EC8CBBE.20106.1E02C435@localhost> Organization: Delft University of Technology (TNW-DCT) MIME-version: 1.0 X-Mailer: Pegasus Mail for Windows (v4.11) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body Priority: normal Hi, I'm trying to find a transition state using G98 and in the last step (before the job finishes because it has found a stationary point) something strange happens. Some of the numbers are question marks instead of numbers, some completely others only partly (see below). Can somebody tell me what is happening? Cheers, Martijn SCF Done: E(RB+HF-LYP) = -1320.15854295 A.U. after 12 cycles Convg = 0.6129D-08 -V/TSCF Done: E(RB+HF-LYP) = -1320.15854295 A.U. after 12 cycles Convg = 0.6129D-08 -V/T = 2.0021 S**2 = 0.0000 KE= 1.317421835399D+03 PE=-4.500952431911D+03 EE= 1.181244953298D+03 Leave Link 502 at Mon May 19 11:45:07 2003, MaxMem= 6291456 cpu: 1551.3 (Enter /opt/g98/g98/l701.exe) Compute integral first derivatives. ... and contract with generalized density number 0. Leave Link 701 at Mon May 19 11:45:08 2003, MaxMem= 6291456 cpu: 0.9 (Enter /opt/g98/g98/l702.exe) L702 exits ... SP integral derivatives will be done elsewhere. Leave Link 702 at Mon May 19 11:45:08 2003, MaxMem= 6291456 cpu: 0.0 (Enter /opt/g98/g98/l703.exe) Compute integral first derivatives. Integral derivatives from FoFDir, PRISM(SPDF). Symmetry not used in FoFDir. MinBra= 0 MaxBra= 2 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. Leave Link 703 at Mon May 19 11:53:48 2003, MaxMem= 6291456 cpu: 519.7 (Enter /opt/g98/g98/l716.exe) ------------------------------------------------------------------- Center Atomic Forces (Hartrees/Bohr) Number Number X Y Z ------------------------------------------------------------------- 1 8 -0.001355822 -0.001942692 -0.001067664 2 14 0.003434706 -0.000108440 -0.001372502 3 8 0.001473467 0.005124041 -0.003343005 4 8 0.000490688 0.002196607 -0.003635757 5 14 -0.006355809 -0.006217662 0.016178221 6 8 -0.003548090 0.002374738 -0.004764821 7 8 0.010380531 -0.001965613 -0.004934520 8 14 -0.004661817 0.000760600 0.003815962 9 8 0.000142147 -0.000221579 -0.000875914 ------------------------------------------------------------------- Cartesian Forces: Max 0.016178221 RMS 0.004844746 Leave Link 716 at Mon May 19 11:53:48 2003, MaxMem= 6291456 cpu: 0.0 (Enter /opt/g98/g98/l103.exe) GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGr ad Berny optimization. Internal Forces: Max 0.000000000 RMS ??????????????? Search for a saddle point. Step number 32 out of a maximum of 65 All quantities printed in internal units (Hartrees-Bohrs-Radians) Update second derivatives using information from points 32 Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvectors required to have negative eigenvalues: R1 R2 R3 R4 R5 1 0.00000 0.00000 0.00000 0.00000 0.00000 R6 R7 R8 R9 R10 1 0.00000 0.00000 0.00000 0.00000 0.00000 R11 A1 A2 A3 A4 1 0.00000 0.00000 0.00000 0.00000 0.00000 A5 A6 A7 A8 A9 1 0.00000 0.00000 0.00000 0.00000 0.00000 A10 A11 A12 A13 A14 1 0.00000 0.00000 0.00000 0.00000 0.00000 A15 A16 A17 A18 A19 1 0.00000 0.00000 0.00000 0.00000 0.00000 D1 D2 D3 D4 D5 1 0.00000 0.00000 0.00000 0.00000 0.00000 D6 D7 D8 D9 D10 1 0.00000 0.00000 0.00000 0.00000 0.00000 D11 D12 D13 D14 D15 1 0.00000 0.00000 0.00000 0.00000 0.00000 D16 D17 D18 D19 D20 1 0.00000 0.00000 0.00000 0.00000 0.00000 D21 D22 D23 D24 D25 1 0.00000 0.00000 0.00000 0.00000 1.00000 QST in optimization variable space. Tangent TS vect // Eig F Eigenval 1 R1 ?????????? 0.00000???????????????????? 2 R2 ?????????? 0.00000???????????????????? 3 R3 ?????????? 0.00000???????????????????? 4 R4 ?????????? 0.00000???????????????????? 5 R5 ?????????? 0.00000???????????????????? 6 R6 ?????????? 0.00000???????????????????? 7 R7 ?????????? 0.00000???????????????????? 8 R8 ?????????? 0.00000???????????????????? 9 R9 ?????????? 0.00000???????????????????? 10 R10 ?????????? 0.00000???????????????????? 11 R11 ?????????? 0.00000???????????????????? 12 A1 ?????????? 0.00000???????????????????? 13 A2 ?????????? 0.00000???????????????????? 14 A3 ?????????? 0.00000???????????????????? 15 A4 ?????????? 0.00000???????????????????? 16 A5 ?????????? 0.00000???????????????????? 17 A6 ?????????? 0.00000???????????????????? 18 A7 ?????????? 0.00000???????????????????? 19 A8 ?????????? 0.00000???????????????????? 20 A9 ?????????? 0.00000???????????????????? 21 A10 ?????????? 0.00000???????????????????? 22 A11 ?????????? 0.00000???????????????????? 23 A12 ?????????? 0.00000???????????????????? 24 A13 ?????????? 0.00000???????????????????? 25 A14 ?????????? 0.00000???????????????????? 26 A15 ?????????? 0.00000???????????????????? 27 A16 ?????????? 0.00000???????????????????? 28 A17 ?????????? 0.00000???????????????????? 29 A18 ?????????? 0.00000???????????????????? 30 A19 ?????????? 0.00000???????????????????? 31 D1 ?????????? 0.00000???????????????????? 32 D2 ?????????? 0.00000???????????????????? 33 D3 ?????????? 0.00000???????????????????? 34 D4 ?????????? 0.00000???????????????????? 35 D5 ?????????? 0.00000???????????????????? 36 D6 ?????????? 0.00000???????????????????? 37 D7 ?????????? 0.00000???????????????????? 38 D8 ?????????? 0.00000???????????????????? 39 D9 ?????????? 0.00000???????????????????? 40 D10 ?????????? 0.00000???????????????????? 41 D11 ?????????? 0.00000???????????????????? 42 D12 ?????????? 0.00000???????????????????? 43 D13 ?????????? 0.00000???????????????????? 44 D14 ?????????? 0.00000???????????????????? 45 D15 ?????????? 0.00000???????????????????? 46 D16 ?????????? 0.00000???????????????????? 47 D17 ?????????? 0.00000???????????????????? 48 D18 ?????????? 0.00000???????????????????? 49 D19 ?????????? 0.00000???????????????????? 50 D20 ?????????? 0.00000???????????????????? 51 D21 ?????????? 0.00000???????????????????? 52 D22 ?????????? 0.00000???????????????????? 53 D23 ?????????? 0.00000???????????????????? 54 D24 ?????????? 0.00000???????????????????? 55 D25 ?????????? 1.00000???????????????????? RFO step: Lambda0=??????????????? Lambda=???????????????. Linear search not attempted -- option 19 set. Iteration 1 RMS(Cart)= 0.00000000 RMS(Int)=???????????? Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total) R1 2.86671?????????? 0.00000?????????? 0.00000 2.86671 R2 3.21056?????????? 0.00000?????????? 0.00000 3.21056 R3 3.08635?????????? 0.00000?????????? 0.00000 3.08635 R4 5.95442?????????? 0.00000?????????? 0.00000 5.95442 R5 3.34526?????????? 0.00000?????????? 0.00000 3.34526 R6 2.87603?????????? 0.00000?????????? 0.00000 2.87603 R7 4.02588?????????? 0.00000?????????? 0.00000 4.02588 R8 2.90355?????????? 0.00000?????????? 0.00000 2.90355 R9 2.85592?????????? 0.00000?????????? 0.00000 2.85592 R10 3.21964?????????? 0.00000?????????? 0.00000 3.21964 R11 7.66083?????????? 0.00000?????????? 0.00000 7.66083 A1 2.27420?????????? 0.00000?????????? 0.00000 2.27420 A2 2.46620?????????? 0.00000?????????? 0.00000 2.46620 A3 1.54001?????????? 0.00000?????????? 0.00000 1.54001 A4 3.14159?????????? 0.00000?????????? 0.00000 3.14159 A5 1.63475?????????? 0.00000?????????? 0.00000 1.63475 A6 1.93792?????????? 0.00000?????????? 0.00000 1.93792 A7 2.84501?????????? 0.00000?????????? 0.00000 2.84501 A8 1.49111?????????? 0.00000?????????? 0.00000 1.49111 A9 2.49479?????????? 0.00000?????????? 0.00000 2.49479 A10 0.88765?????????? 0.00000?????????? 0.00000 0.88765 A11 2.28968?????????? 0.00000?????????? 0.00000 2.28968 A12 3.10463?????????? 0.00000?????????? 0.00000 3.10463 A13 1.63673?????????? 0.00000?????????? 0.00000 1.63673 A14 1.46225?????????? 0.00000?????????? 0.00000 1.46225 A15 2.88036?????????? 0.00000?????????? 0.00000 2.88036 A16 1.39575?????????? 0.00000?????????? 0.00000 1.39575 A17 1.00387?????????? 0.00000?????????? 0.00000 1.00387 A18 0.01354?????????? 0.00000?????????? 0.00000 0.01354 A19 3.09954?????????? 0.00000?????????? 0.00000 3.09954 D1 -1.61048?????????? 0.00000?????????? 0.00000 - 1.61048 D2 1.46364?????????? 0.00000?????????? 0.00000 1.46364 D3 2.96215?????????? 0.00000?????????? 0.00000 2.96215 D4 -0.09711?????????? 0.00000?????????? 0.00000 - 0.09711 D5 -1.35135?????????? 0.00000?????????? 0.00000 - 1.35135 D6 1.77793?????????? 0.00000?????????? 0.00000 1.77793 D7 -3.00589?????????? 0.00000?????????? 0.00000 - 3.00589 D8 0.39497?????????? 0.00000?????????? 0.00000 0.39497 D9 -0.27861?????????? 0.00000?????????? 0.00000 - 0.27861 D10 3.10540?????????? 0.00000?????????? 0.00000 3.10540 D11 -0.01505?????????? 0.00000?????????? 0.00000 - 0.01505 D12 -2.90325?????????? 0.00000?????????? 0.00000 - 2.90325 D13 -2.97320?????????? 0.00000?????????? 0.00000 - 2.97320 D14 0.10092?????????? 0.00000?????????? 0.00000 0.10092 D15 -0.09359?????????? 0.00000?????????? 0.00000 - 0.09359 D16 2.90901?????????? 0.00000?????????? 0.00000 2.90901 D17 3.13514?????????? 0.00000?????????? 0.00000 3.13514 D18 0.09736?????????? 0.00000?????????? 0.00000 0.09736 D19 0.21353?????????? 0.00000?????????? 0.00000 0.21353 D20 -3.07616?????????? 0.00000?????????? 0.00000 - 3.07616 D21 -0.00980?????????? 0.00000?????????? 0.00000 - 0.00980 D22 0.02193?????????? 0.00000?????????? 0.00000 0.02193 D23 1.55440?????????? 0.00000?????????? 0.00000 1.55440 D24 -2.61785?????????? 0.00000?????????? 0.00000 - 2.61785 D25 -1.55304?????????? 0.00000?????????? 0.00000 - 1.55304 Item Value Threshold Converged? Maximum Force 0.000000 0.000450 YES RMS Force ???????? 0.000300 YES Maximum Displacement 0.000000 0.001800 YES RMS Displacement 0.000000 0.001200 YES Predicted change in Energy= 0.000000D+00 Optimization completed. -- Stationary point found.---------------------------------------- --------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@ccl.net Mon May 19 12:10:35 2003 Received: from ccl.net (pagergate.ccl.net [192.148.249.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4JGAZo8017234 for ; Mon, 19 May 2003 12:10:35 -0400 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.1) with ESMTP id h4JGAXt02203; Mon, 19 May 2003 12:10:33 -0400 (EDT) Date: Mon, 19 May 2003 12:10:32 -0400 (EDT) From: Jan Labanowski To: chemistry{at}ccl.net cc: jkl{at}ccl.net Subject: CCL: Disruption in CCL operation (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL members... Your sleepy coordinator speaks in a faint voice... I also smell bad {:-(}. I thought it will be a short job, but things always take more than you wish. With the spammers attacking CCL like mad dogs, I had to take some measures. For this reason, the CCL server has been moved to another machine running RH9.0 with most security updates installed. I started about 11pm yesterday, and I need to go to bed soon, since I do not see much. But I still have many things to do, and need to process the backlog of mail. Now, before you post to CCL, you need to put CCL: on the Subject line. This way your script will only go through routine/automatic checks before it is posted. If the checks do not find anything even slightly suspicious, they will let the message through. If they find something, the message will be manually reviewed by a human. If you forget about CCL: on the Subject line, your message will need to wait for human to review it. Also... From now on, the e-mail addresses appearing in the message will be intentionally messed up before being SAVED in the CCL archives. I will also do a global replace on the e-mail addresses currently in the archives, but I probably will not be able to get to it today. The @ sign which appears in each e-mail address (oh well, they do not use bangs anymore...) will be replaced by a randomly chosen "look alike" > from the set of twenty, or so of them (e.g., with *at*, (at), -.at.-, etc). We probably should do a competition for good at-look-alikes. The humans will figure out what the e-mail address is, but the automatic harvesting robots will have problems. They are oriented on volume harvest, and hopefully collect only the regular addresses with correct syntax. I could do GIF imges with addresses, but then it would be a problem with plain text files. The footnote to each CCL message became longer, I will hopefully condense it some day. I also need to update the instructions on the Web and info for new subscribers. I will be discontinuing e-mail based services like MAILSERVER (serving files from CCL archives via e-mail) and e-mail based CCL archive search. Since currently THERE IS NO WAY to establish identity of the party originating the e-mail, the stupid spammers try to use these services to include junk mail into the request with phony From: address hoping for it to bounce. While it does not really work, they still manage to produce error codes which are sent to unsuspecting people. On top of this, due to formidable economic boom, I do not have really any help in doing the chores. So, please be considerate, or send me donations to CCL fund (just go to CCL Home page, read how you can give me money or buy something from CCL, and roll the green my way {:-(}.. Will be much obliged...). Thank you for your patience... Jan jkl@ccl.net Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | E-mail: jkl{at}ccl.net 1224 Kinnear Rd, | http://www.ccl.net/~jkl Columbus, OH 43212-1163 | http://www.ccl.net/ http://asdn.net/ From chemistry-request@ccl.net Mon May 19 06:19:32 2003 Received: from ns2.tudelft.nl (ns2.tudelft.nl [130.161.180.65]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4JAJVo8030972 for ; Mon, 19 May 2003 06:19:32 -0400 Received: from CONVERSION-DAEMON.mailhost1.tudelft.nl by mailhost1.tudelft.nl (PMDF V6.1-1 #40924) id <0HF400501Q0G4V.-at-.mailhost1.tudelft.nl> for chemistry.-at-.ccl.net; Mon, 19 May 2003 12:19:29 +0200 (MEST) Received: from mail.dct.tudelft.nl (mail.dct.tudelft.nl [130.161.196.201]) by mailhost1.tudelft.nl (PMDF V6.1-1 #40924) with ESMTP id <0HF400EM0Q0FMK.-at-.mailhost1.tudelft.nl> for chemistry.-at-.ccl.net; Mon, 19 May 2003 12:19:27 +0200 (MEST) Received: from TNW-DCT1/SpoolDir by mail.dct.tudelft.nl (Mercury 1.48); Mon, 19 May 2003 12:19:27 +0200 Received: from SpoolDir by TNW-DCT1 (Mercury 1.48); Mon, 19 May 2003 12:19:22 +0200 Date: Mon, 19 May 2003 12:19:17 +0200 From: Martijn Zwijnenburg Subject: ? in G98 output To: chemistry.-at-.ccl.net Message-id: <3EC8CBBE.20106.1E02C435@localhost> Organization: Delft University of Technology (TNW-DCT) MIME-version: 1.0 X-Mailer: Pegasus Mail for Windows (v4.11) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body Priority: normal Hi, I'm trying to find a transition state using G98 and in the last step (before the job finishes because it has found a stationary point) something strange happens. Some of the numbers are question marks instead of numbers, some completely others only partly (see below). Can somebody tell me what is happening? Cheers, Martijn SCF Done: E(RB+HF-LYP) = -1320.15854295 A.U. after 12 cycles Convg = 0.6129D-08 -V/TSCF Done: E(RB+HF-LYP) = -1320.15854295 A.U. after 12 cycles Convg = 0.6129D-08 -V/T = 2.0021 S**2 = 0.0000 KE= 1.317421835399D+03 PE=-4.500952431911D+03 EE= 1.181244953298D+03 Leave Link 502 at Mon May 19 11:45:07 2003, MaxMem= 6291456 cpu: 1551.3 (Enter /opt/g98/g98/l701.exe) Compute integral first derivatives. ... and contract with generalized density number 0. Leave Link 701 at Mon May 19 11:45:08 2003, MaxMem= 6291456 cpu: 0.9 (Enter /opt/g98/g98/l702.exe) L702 exits ... SP integral derivatives will be done elsewhere. Leave Link 702 at Mon May 19 11:45:08 2003, MaxMem= 6291456 cpu: 0.0 (Enter /opt/g98/g98/l703.exe) Compute integral first derivatives. Integral derivatives from FoFDir, PRISM(SPDF). Symmetry not used in FoFDir. MinBra= 0 MaxBra= 2 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. Leave Link 703 at Mon May 19 11:53:48 2003, MaxMem= 6291456 cpu: 519.7 (Enter /opt/g98/g98/l716.exe) ------------------------------------------------------------------- Center Atomic Forces (Hartrees/Bohr) Number Number X Y Z ------------------------------------------------------------------- 1 8 -0.001355822 -0.001942692 -0.001067664 2 14 0.003434706 -0.000108440 -0.001372502 3 8 0.001473467 0.005124041 -0.003343005 4 8 0.000490688 0.002196607 -0.003635757 5 14 -0.006355809 -0.006217662 0.016178221 6 8 -0.003548090 0.002374738 -0.004764821 7 8 0.010380531 -0.001965613 -0.004934520 8 14 -0.004661817 0.000760600 0.003815962 9 8 0.000142147 -0.000221579 -0.000875914 ------------------------------------------------------------------- Cartesian Forces: Max 0.016178221 RMS 0.004844746 Leave Link 716 at Mon May 19 11:53:48 2003, MaxMem= 6291456 cpu: 0.0 (Enter /opt/g98/g98/l103.exe) GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGr ad Berny optimization. Internal Forces: Max 0.000000000 RMS ??????????????? Search for a saddle point. Step number 32 out of a maximum of 65 All quantities printed in internal units (Hartrees-Bohrs-Radians) Update second derivatives using information from points 32 Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvalues --- ?????????????????????????????????????????????????? Eigenvectors required to have negative eigenvalues: R1 R2 R3 R4 R5 1 0.00000 0.00000 0.00000 0.00000 0.00000 R6 R7 R8 R9 R10 1 0.00000 0.00000 0.00000 0.00000 0.00000 R11 A1 A2 A3 A4 1 0.00000 0.00000 0.00000 0.00000 0.00000 A5 A6 A7 A8 A9 1 0.00000 0.00000 0.00000 0.00000 0.00000 A10 A11 A12 A13 A14 1 0.00000 0.00000 0.00000 0.00000 0.00000 A15 A16 A17 A18 A19 1 0.00000 0.00000 0.00000 0.00000 0.00000 D1 D2 D3 D4 D5 1 0.00000 0.00000 0.00000 0.00000 0.00000 D6 D7 D8 D9 D10 1 0.00000 0.00000 0.00000 0.00000 0.00000 D11 D12 D13 D14 D15 1 0.00000 0.00000 0.00000 0.00000 0.00000 D16 D17 D18 D19 D20 1 0.00000 0.00000 0.00000 0.00000 0.00000 D21 D22 D23 D24 D25 1 0.00000 0.00000 0.00000 0.00000 1.00000 QST in optimization variable space. Tangent TS vect // Eig F Eigenval 1 R1 ?????????? 0.00000???????????????????? 2 R2 ?????????? 0.00000???????????????????? 3 R3 ?????????? 0.00000???????????????????? 4 R4 ?????????? 0.00000???????????????????? 5 R5 ?????????? 0.00000???????????????????? 6 R6 ?????????? 0.00000???????????????????? 7 R7 ?????????? 0.00000???????????????????? 8 R8 ?????????? 0.00000???????????????????? 9 R9 ?????????? 0.00000???????????????????? 10 R10 ?????????? 0.00000???????????????????? 11 R11 ?????????? 0.00000???????????????????? 12 A1 ?????????? 0.00000???????????????????? 13 A2 ?????????? 0.00000???????????????????? 14 A3 ?????????? 0.00000???????????????????? 15 A4 ?????????? 0.00000???????????????????? 16 A5 ?????????? 0.00000???????????????????? 17 A6 ?????????? 0.00000???????????????????? 18 A7 ?????????? 0.00000???????????????????? 19 A8 ?????????? 0.00000???????????????????? 20 A9 ?????????? 0.00000???????????????????? 21 A10 ?????????? 0.00000???????????????????? 22 A11 ?????????? 0.00000???????????????????? 23 A12 ?????????? 0.00000???????????????????? 24 A13 ?????????? 0.00000???????????????????? 25 A14 ?????????? 0.00000???????????????????? 26 A15 ?????????? 0.00000???????????????????? 27 A16 ?????????? 0.00000???????????????????? 28 A17 ?????????? 0.00000???????????????????? 29 A18 ?????????? 0.00000???????????????????? 30 A19 ?????????? 0.00000???????????????????? 31 D1 ?????????? 0.00000???????????????????? 32 D2 ?????????? 0.00000???????????????????? 33 D3 ?????????? 0.00000???????????????????? 34 D4 ?????????? 0.00000???????????????????? 35 D5 ?????????? 0.00000???????????????????? 36 D6 ?????????? 0.00000???????????????????? 37 D7 ?????????? 0.00000???????????????????? 38 D8 ?????????? 0.00000???????????????????? 39 D9 ?????????? 0.00000???????????????????? 40 D10 ?????????? 0.00000???????????????????? 41 D11 ?????????? 0.00000???????????????????? 42 D12 ?????????? 0.00000???????????????????? 43 D13 ?????????? 0.00000???????????????????? 44 D14 ?????????? 0.00000???????????????????? 45 D15 ?????????? 0.00000???????????????????? 46 D16 ?????????? 0.00000???????????????????? 47 D17 ?????????? 0.00000???????????????????? 48 D18 ?????????? 0.00000???????????????????? 49 D19 ?????????? 0.00000???????????????????? 50 D20 ?????????? 0.00000???????????????????? 51 D21 ?????????? 0.00000???????????????????? 52 D22 ?????????? 0.00000???????????????????? 53 D23 ?????????? 0.00000???????????????????? 54 D24 ?????????? 0.00000???????????????????? 55 D25 ?????????? 1.00000???????????????????? RFO step: Lambda0=??????????????? Lambda=???????????????. Linear search not attempted -- option 19 set. Iteration 1 RMS(Cart)= 0.00000000 RMS(Int)=???????????? Variable Old X -DE/DX Delta X Delta X Delta X New X (Linear) (Quad) (Total) R1 2.86671?????????? 0.00000?????????? 0.00000 2.86671 R2 3.21056?????????? 0.00000?????????? 0.00000 3.21056 R3 3.08635?????????? 0.00000?????????? 0.00000 3.08635 R4 5.95442?????????? 0.00000?????????? 0.00000 5.95442 R5 3.34526?????????? 0.00000?????????? 0.00000 3.34526 R6 2.87603?????????? 0.00000?????????? 0.00000 2.87603 R7 4.02588?????????? 0.00000?????????? 0.00000 4.02588 R8 2.90355?????????? 0.00000?????????? 0.00000 2.90355 R9 2.85592?????????? 0.00000?????????? 0.00000 2.85592 R10 3.21964?????????? 0.00000?????????? 0.00000 3.21964 R11 7.66083?????????? 0.00000?????????? 0.00000 7.66083 A1 2.27420?????????? 0.00000?????????? 0.00000 2.27420 A2 2.46620?????????? 0.00000?????????? 0.00000 2.46620 A3 1.54001?????????? 0.00000?????????? 0.00000 1.54001 A4 3.14159?????????? 0.00000?????????? 0.00000 3.14159 A5 1.63475?????????? 0.00000?????????? 0.00000 1.63475 A6 1.93792?????????? 0.00000?????????? 0.00000 1.93792 A7 2.84501?????????? 0.00000?????????? 0.00000 2.84501 A8 1.49111?????????? 0.00000?????????? 0.00000 1.49111 A9 2.49479?????????? 0.00000?????????? 0.00000 2.49479 A10 0.88765?????????? 0.00000?????????? 0.00000 0.88765 A11 2.28968?????????? 0.00000?????????? 0.00000 2.28968 A12 3.10463?????????? 0.00000?????????? 0.00000 3.10463 A13 1.63673?????????? 0.00000?????????? 0.00000 1.63673 A14 1.46225?????????? 0.00000?????????? 0.00000 1.46225 A15 2.88036?????????? 0.00000?????????? 0.00000 2.88036 A16 1.39575?????????? 0.00000?????????? 0.00000 1.39575 A17 1.00387?????????? 0.00000?????????? 0.00000 1.00387 A18 0.01354?????????? 0.00000?????????? 0.00000 0.01354 A19 3.09954?????????? 0.00000?????????? 0.00000 3.09954 D1 -1.61048?????????? 0.00000?????????? 0.00000 - 1.61048 D2 1.46364?????????? 0.00000?????????? 0.00000 1.46364 D3 2.96215?????????? 0.00000?????????? 0.00000 2.96215 D4 -0.09711?????????? 0.00000?????????? 0.00000 - 0.09711 D5 -1.35135?????????? 0.00000?????????? 0.00000 - 1.35135 D6 1.77793?????????? 0.00000?????????? 0.00000 1.77793 D7 -3.00589?????????? 0.00000?????????? 0.00000 - 3.00589 D8 0.39497?????????? 0.00000?????????? 0.00000 0.39497 D9 -0.27861?????????? 0.00000?????????? 0.00000 - 0.27861 D10 3.10540?????????? 0.00000?????????? 0.00000 3.10540 D11 -0.01505?????????? 0.00000?????????? 0.00000 - 0.01505 D12 -2.90325?????????? 0.00000?????????? 0.00000 - 2.90325 D13 -2.97320?????????? 0.00000?????????? 0.00000 - 2.97320 D14 0.10092?????????? 0.00000?????????? 0.00000 0.10092 D15 -0.09359?????????? 0.00000?????????? 0.00000 - 0.09359 D16 2.90901?????????? 0.00000?????????? 0.00000 2.90901 D17 3.13514?????????? 0.00000?????????? 0.00000 3.13514 D18 0.09736?????????? 0.00000?????????? 0.00000 0.09736 D19 0.21353?????????? 0.00000?????????? 0.00000 0.21353 D20 -3.07616?????????? 0.00000?????????? 0.00000 - 3.07616 D21 -0.00980?????????? 0.00000?????????? 0.00000 - 0.00980 D22 0.02193?????????? 0.00000?????????? 0.00000 0.02193 D23 1.55440?????????? 0.00000?????????? 0.00000 1.55440 D24 -2.61785?????????? 0.00000?????????? 0.00000 - 2.61785 D25 -1.55304?????????? 0.00000?????????? 0.00000 - 1.55304 Item Value Threshold Converged? Maximum Force 0.000000 0.000450 YES RMS Force ???????? 0.000300 YES Maximum Displacement 0.000000 0.001800 YES RMS Displacement 0.000000 0.001200 YES Predicted change in Energy= 0.000000D+00 Optimization completed. -- Stationary point found.---------------------------------------- --------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg.-at-.tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@ccl.net Mon May 19 12:59:43 2003 Received: from frontend-1.cgpmail.ua.pt (mail.ua.pt [193.136.80.79]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4JGxgo8021386 for ; Mon, 19 May 2003 12:59:43 -0400 X-UA: Message Inspected for Viruses by RAV Received: from [192.168.69.132] (HELO backend-2.cgpmail.ua.pt) by frontend-1.cgpmail.ua.pt (CommuniGate Pro SMTP 4.0.6) with ESMTP id 9610563 for chemistry..at..ccl.net; Mon, 19 May 2003 17:59:37 +0100 Received: from [193.136.83.38] (account ) by backend-2.cgpmail.ua.pt (CommuniGate Pro WebUser 4.0.6) with HTTP id 5330297 for ; Mon, 19 May 2003 17:56:41 +0100 From: "Nelson Fonseca" Subject: CCL: Morokuma energy decomposition in g98 To: X-Mailer: CommuniGate Pro Web Mailer v.4.0.6 Date: Mon, 19 May 2003 17:56:41 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Content-Transfer-Encoding: 8bit Experience is what you get when you don't get what you want. -- Dan Stanford-- dear all: I would like to know if the Morokuma energy decomposition scheme is implemented in Gaussian 98. I think that in GAMESS this scheme is present. Thanks in advance best regards nelson fonseca University of Aveiro Portugal From chemistry-request@ccl.net Mon May 19 14:17:02 2003 Received: from celebris04.cetem.gov.br (correio.cetem.gov.br [200.20.105.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4JIH1o8026936 for ; Mon, 19 May 2003 14:17:01 -0400 Received: by correio.cetem.gov.br with Internet Mail Service (5.5.2653.19) id ; Mon, 19 May 2003 15:18:47 -0300 Message-ID: <216FE3CA3D4DD611AE2600105AD16BDFD56B33*at*correio.cetem.gov.br> From: Ian Hovell To: =?iso-8859-1?Q?Chemistry_=28Correio_eletr=F4nico=29?= Subject: CCL:scipcm job fails to complete Date: Mon, 19 May 2003 15:18:47 -0300 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h4JIH2o8026941 Dear CCLers, Below is an edited output from a failed gaussian job. It fails stating: ShPair-CalcS2-2 allocation failure: I have been unable to find any reference to this in the manual. Can any body shed any light on this problem TIA Ian %mem=10MW %nproc=1 Will use up to 1 processors via shared memory. Default route: MaxDisk=2000MB ------------------------------------------ # rhf/3-21g* scrf=scipcm geom=connectivity ------------------------------------------ 1/38=1,57=2/1; 2/17=6,18=5,40=1/2; 3/5=5,7=1,11=1,25=1,30=1/1,2,3; 4/7=1/1; 5/5=2,32=1,38=4,40=1000/2; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; ----------------------------------- Solvated Solutes: hydroxyquinaldine ----------------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C C 1 1.3604 C 2 1.42079 1 119.7042 C 3 1.40232 2 118.70315 1 0.34555 0 C 4 1.41382 3 120.51752 2 -0.18059 0 C 5 1.35698 4 119.39375 3 0.01308 0 H 1 1.07087 2 119.8106 3 179.80729 0 N 3 1.36706 2 119.24129 1 -179.8798 0 C 4 1.42029 3 117.18863 2 179.53833 0 H 5 1.07213 4 119.27995 3 179.97652 0 H 6 1.07187 5 120.4652 4 -179.87495 0 C 9 1.351 4 119.63294 3 -0.08886 0 C 8 1.30384 3 119.65922 2 -179.2798 0 H 9 1.07275 4 119.13639 3 -179.92619 0 H 12 1.07142 9 121.24498 4 -179.79238 0 O 2 1.36814 1 123.62778 6 179.62457 0 H 16 0.96618 2 113.32298 1 -0.66918 0 C 13 1.51008 8 120.08982 3 179.47196 0 H 18 1.08504 13 110.04764 8 -121.81192 0 H 18 1.07866 13 110.46305 8 -1.29531 0 H 18 1.08544 13 110.22502 8 119.45484 0 ---------------------------Cut out put---------------------------- Projected INDO Guess. Warning! Cutoffs for single-point calculations used. Requested convergence on RMS density matrix=1.00D-04 within 64 cycles. Requested convergence on MAX density matrix=1.00D-02. Requested convergence on energy=5.00D-05. ShPair-CalcS2-2 allocation failure: iend,mxcore= 166464 137127 Error termination via Lnk1e in C:\G98W\l502.exe. Job cpu time: 0 days 0 hours 13 minutes 28.0 seconds. File lengths (MBytes): RWF= 14 Int= 0 D2E= 0 Chk= 1 Scr= 1 Ian Hovell - Ph.D. NUCLEO DE MODELAGEM MOLECULAR-NMM Centro de Tecnologia Mineral - CETEM Ministerio da Cijncia e da Tecnologia- MCT Avenida Ipj, No 900 - Cidade Universitaria Ilha do Fundco Rio de Janeiro RJ Brasil CEP 21941-590 tel 00 55 (xx) 3865 - 7216 Fax 00 55 (xx) 22602837 ou 2290-4286 e-mail hovell*at*cetem.gov.br From chemistry-request@ccl.net Mon May 19 17:47:17 2003 Received: from julesburg.uits.indiana.edu (julesburg.uits.indiana.edu [129.79.1.75]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h4JLlHo8009213 for ; Mon, 19 May 2003 17:47:17 -0400 Received: from auggiedoggie.uits.iupui.edu (auggiedoggie.uits.iupui.edu [134.68.220.202]) by julesburg.uits.indiana.edu (8.12.9/8.12.9/IUPO) with ESMTP id h4JLlE3q001844 for ; Mon, 19 May 2003 16:47:14 -0500 (EST) Received: from iupui.edu ([134.68.57.154]) by auggiedoggie.uits.iupui.edu (8.12.9/8.12.9/IUPUIPO.20030331) with ESMTP id h4JLlG93003606 for ; Mon, 19 May 2003 16:47:16 -0500 (EST) Sender: qin_at_auggiedoggie.uits.iupui.edu Message-ID: <3EC950EA.AEFF7FED_at_iupui.edu> Date: Mon, 19 May 2003 16:47:22 -0500 From: "Q.Z." X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.7-10 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry_at_ccl.net Subject: CCL: Autodock: how to minimize the protein structure alone] Content-Type: multipart/mixed; boundary="------------79EC0E27D2F4CFE10481F4AD" This is a multi-part message in MIME format. --------------79EC0E27D2F4CFE10481F4AD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit let me try again using CCL: header. --------------79EC0E27D2F4CFE10481F4AD Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit Content-Disposition: inline X-Mozilla-Status2: 00000000 Message-ID: <3EC949C2.C8579BDE_at_iupui.edu> Date: Mon, 19 May 2003 16:16:51 -0500 From: "Q.Z." X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.7-10 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry_at_ccl.net Subject: Autodock: how to minimize the protein structure alone Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I am trying to use the same force field that is used for the autodock to minimize the protein structure before docking. The autodock 3.0 manual shows that there is an option of " do-local-only" for the autodock3 command. But I was not sure that is to only minimize the protein or the protein-ligand complex or just the ligand. Also is there a similar option in ADT interface? Thanks. Q. Zou, Ph D. Indiana University Schl. of Med. --------------79EC0E27D2F4CFE10481F4AD--