From chemistry-request@server.ccl.net Thu Feb 8 00:33:55 2001 Received: from cascara.UVic.CA (root@cascara.uvic.ca [142.104.5.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f185Xsw05943 for ; Thu, 8 Feb 2001 00:33:55 -0500 Received: from p17-90.dialup.uvic.ca (p17-90.dialup.uvic.ca [142.104.17.90]) by cascara.UVic.CA (8.11.2/8.11.2) with SMTP id f185Xor126822 for ; Wed, 7 Feb 2001 21:33:51 -0800 From: Roy Jensen To: chemistry@ccl.net Subject: SUMMARY: Transition State Optimization Date: Wed, 07 Feb 2001 21:35:56 -0800 Message-ID: <91c48t4h96kk47vjsorgh4m7r3p4tro5vo@4ax.com> X-Mailer: Forte Agent 1.8/32.548 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f185Xtw05944 I wont summarize the individual responses, they were all the same: 1. Use the NOEIGENTEST keyword. 2. You have to be close to the TS for this to converge in 20 iterations. Look at the output file, manually adjust the geometry, and try again. 3. Once the geometry is very close to the TS, removing the NOEIGENTEST keyword _might_ work. If it does, the job will converge faster. In summary, it is not a one-step job -- you have to work at it. NOTE: I did try the NOEIGENTEST keyword before posting my question, but the job did not optimize. As stated above, I was too far from the transition state. Thanks to all, Roy Jensen ORIGINAL POST ============= > I am attempting a transition state optimization on G98W A.9, currently on > HOCN. Using a multitude of methods, basis sets, and starting geometries, > I fail to get a negative eigenvalue after the first step. The exact error: > -- Wrong number of Negative eigenvalues: Desired= 1 Actual= 0 > > Has anyone experienced this problem? > An input file is copied below. > > Roy Jensen From chemistry-request@server.ccl.net Wed Feb 7 17:51:52 2001 Received: from mail.rpi.edu (root@mail.rpi.edu [128.113.100.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f17Mpqw03003 for ; Wed, 7 Feb 2001 17:51:52 -0500 Received: from curtp5 (curtp5.chem.rpi.edu [128.113.21.59]) by mail.rpi.edu (8.9.3/8.9.3) with SMTP id RAA675628; Wed, 7 Feb 2001 17:51:50 -0500 Message-ID: <3A81D0BC.4B47@rpi.edu> Date: Wed, 07 Feb 2001 17:48:28 -0500 From: "Curt M. Breneman" Reply-To: brenec@rpi.edu Organization: RPI Department of Chemistry X-Mailer: Mozilla 3.02 (WinNT; I) MIME-Version: 1.0 To: chemistry@ccl.net CC: brenec@rpi.edu Subject: Announcement - CCG Graduate Student Travel Awards. Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Announcement: The Division of Computers and Chemistry (COMP) is pleased to announce another round of five Chemical Computing Group (CCG) Excellence Awards. These awards were created to stimulate graduate student participation in COMP Division activities (symposia and poster sessions) at ACS National Meetings. Winners will receive one-year licenses of CCG's MOE software for their research groups in addition to their travel reimbursements. You may apply for the CCG Excellence Award by submitting an abstract of your poster or presentation to me along with a letter of support from your research advisor, a two-page CV and a personal statement. The awardees will be chosen on the basis of the quality and significance of the research to be presented and the strength of the supporting materials. The Awards will each cover up to US $1,150 of the travel costs associated with attending an ACS National Meeting - in this case, the Spring 2001 meeting in San Diego, CA. The deadline for submission of all materials is February 28, 2001. Winners will be selected by March 15, 2001. Please submit materials to: Prof. Curt M. Breneman RPI Department of Chemistry 110 8th St, Troy, NY 12180 USA Thanks for your interest. Curt Breneman RPI Chemistry COMP Treasurer From chemistry-request@server.ccl.net Wed Feb 7 19:06:22 2001 Received: from kafka.net.nih.gov (kafka.net.nih.gov [165.112.130.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1806Hw03495 for ; Wed, 7 Feb 2001 19:06:17 -0500 Received: from I.T.S.ME ([129.43.27.170]) by kafka.net.nih.gov (8.10.1/8.10.1) with ESMTP id f1806H200277; Wed, 7 Feb 2001 19:06:17 -0500 (EST) Date: Wed, 7 Feb 2001 19:04:44 -0500 (Eastern Standard Time) From: "M. Nicklaus" To: CHEMISTRY@ccl.net cc: mn1@helix.nih.gov Subject: Announcement: Enhanced NCI Open Database Browser Release 2 Message-ID: X-X-Sender: mn1@helix.nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The Erlangen/Bethesda Data Services, a collaboration between the CADD Group of the Laboratory of Medicinal Chemistry, NCI, NIH, and the Computer Chemistry Center at the University of Erlangen-Nuremberg, are pleased to announce Release 2 of the Enhanced NCI Database Browser for public beta testing. This service, based on the chemical information toolkit CACTVS, offers searches in the public dataset of over 250,000 open NCI database compounds. Numerous new features have been implemented, approx. 4,000 structures added, and a very large number of additional data calculated and added to the database of searchable information. Here is a *partial* list of the new features and improvements: - New GUI (window switching instead of multiple windows) - Continuation of search now possible if end of database was not reached - Hit list manager to store, intersect, add, subtract etc. hitlists - New substructure search capabilities (e.g., search for H-bond acceptor/donor) - Many more, and/or improved, searchable criteria (log P [calc.], complexity, data availability...) - Names added for approx. 220,000 structures (w/ ACD/Name; thanks to ACD/Labs) - PASS activity spectrum predictions (>500 mechanisms of action; most compounds; Prof. Vladimir Poroikov, Russ. Acad. Med. Sci., Moscow). These are more than 64,000,000 searchable data items. - Links to additional other services for further processing of search results - PubMed - NTP - NIST WebBook - COMPARE - ChemFinder ....and others - Additions and improvements to the output features - MDL Chime for structures, conformers, and hitlists - 3D Java Viewer - VRML Scene - Several spreadsheet formats for hitlists - Additional data can now be exported together with the structures, e.g. in an SD file with added fields - SMILES output is now Unique SMILES (Daylight, JCICS 1989) - 3D pharmacophore search, in up to 25 conformers per compound The site is fully functional, i.e. all data are available, and all search funtionality has been implemented. The current beta testing period is intended to allow for bug fixes, polishing of the interface and help/FAQ texts, and implementation (possibly) of minor changes requested by users (althought we don't want to *promise* anything in this regard). Although the Help page is not yet fully finished, it already contains a lot of useful information. Please have a look at it to learn about the things you can do with the new service. The raw files used to build this service are downloadable from this site in SD and SMILES formats. Also available, at either mirror, are several additional services that people may find useful. The URLs for the service are: http://cactus.nci.nih.gov (U.S. mirror) http://www2.ccc.uni-erlangen.de/ncidb2 (German mirror) Please let us know what your experiences are with these services, positive or negative. (Note pertaining to the recent discussion of "Linux 2.4.0 and 2 GB problem" on the CCL: The new database file is about 3.5 GB. Therefore, on the U.S. mirror (a Linux box), a 2.4.0 kernel was necessary. After some performance problems experienced with the use of the mmap64() system call, work-arounds both in the program and the data structures have solved this problem. Note that this is on an ext2 file system, not on xfs or ReiserFS. See also the separate posting by Wolf-Dietrich Ihlenfeldt on this subject.) Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, Institute for Organic Chemistry, University of Erlangen-Nuremberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 http://www2.ccc.uni-erlangen.de/wdi/ and ------------------------------------------------------------------------ Marc C. Nicklaus National Institutes of Health E-mail: mn1@helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm Laboratory of Medicinal Chemistry, National Cancer Institute, FCRDC ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Feb 8 00:33:58 2001 Received: from cascara.UVic.CA (root@cascara.uvic.ca [142.104.5.28]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f185Xvw05949 for ; Thu, 8 Feb 2001 00:33:57 -0500 Received: from p17-90.dialup.uvic.ca (p17-90.dialup.uvic.ca [142.104.17.90]) by cascara.UVic.CA (8.11.2/8.11.2) with SMTP id f185Xvr208492 for ; Wed, 7 Feb 2001 21:33:57 -0800 From: Roy Jensen To: chemistry@ccl.net Subject: SLATERDET keyword in Gaussian 98 (again) Date: Wed, 07 Feb 2001 21:36:02 -0800 Message-ID: X-Mailer: Forte Agent 1.8/32.548 MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f185Xww05950 I had two people want me to summarize my responses...but no responses! The question is still open. > I am trying to find a singlet-triplet crossing. > > Has anyone sucessfully used the SLATERDET keyword to accomplish this? > Are there any other ways to estimate the crossing? Thanks, Roy Jensen From chemistry-request@server.ccl.net Thu Feb 8 02:50:31 2001 Received: from hpc.biu.ac.il (hpc.biu.ac.il [132.70.185.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f187oQw06399 for ; Thu, 8 Feb 2001 02:50:27 -0500 Received: (from aped@localhost) by hpc.biu.ac.il (AIX4.3/UCB 8.8.8/8.8.8) id JAA39724 for chemistry@server.ccl.net; Thu, 8 Feb 2001 09:50:21 +0200 From: Pinchas Aped Message-Id: <200102080750.JAA39724@hpc.biu.ac.il> Subject: The "ModRedundant" keyword in Gaussian-98 To: chemistry@server.ccl.net Date: Thu, 8 Feb 2001 09:50:16 +0200 (IST) X-Mailer: ELM [version 2.4ME+ PL66s (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear netters: Dear Sir: We have run into a problem running Gaussian 98 (A7): When we try to use the keyword "Geom=ModRedundant" to alter the initial geometry, the resulted "corrected" geometry does not match the required one (as can be seen in the Distance matrix). The same step was executed correctly by Gaussian 94 (we still keep this version for comparison!). We have tried to ask the Gaussian people, but got no response. Attached are the g94 and g98 input and output files. Thank you in advance Pinchas Aped ------------------------ Gaussian98 input file ------------------------ %mem=6000000 #P am1 Geom=ModRedundant guess=only mogi + oh + methyl M4 0 9 fe1 1.770696 -0.620872 0.034366 fe2 -0.556373 1.046257 0.383542 o3 1.036088 0.935867 1.095772 o4 -0.203059 -0.487160 -0.875498 o5 2.159733 0.832370 -1.423820 o6 0.265168 2.170412 -1.226610 o7 0.719070 -1.789751 1.420686 o8 -1.229301 -0.539630 1.674985 c9 1.430701 1.868050 -1.720501 h10 1.843240 2.561341 -2.476997 c11 -0.417949 -1.512791 1.988735 h12 -0.730527 -2.172832 2.818607 n13 3.518309 -0.929948 0.678147 h14 3.728644 -1.536850 1.477530 h15 4.335516 -0.371291 0.409795 n16 -1.148296 2.454376 1.526298 h17 -0.506937 3.261454 1.546103 h18 -1.326524 2.135130 2.490934 o19 1.844883 -2.046665 -1.547295 h20 1.220885 -1.783718 -2.257218 h21 2.690935 -2.415288 -1.870971 o22 -2.365603 1.086648 -0.850145 h23 -2.065430 0.894447 -1.765209 h24 -2.869804 1.926948 -0.789241 h25 -0.794025 -1.256447 -0.708370 c26 -3.852707 -1.857677 0.019899 h27 -3.414307 -0.857891 -0.004004 h28 -4.033471 -2.483570 0.897901 f29 -4.686163 -2.163435 -1.078088 19 13 3.0000 F 22 16 3.0000 F 26 4 5.0000 F 29 22 5.0000 F 4 1 2.1775 F 4 2 2.0153 F 25 4 0.9844 F 27 26 1.0919 F 28 26 1.0933 F 29 26 1.4120 F ------------------- (part of) Gaussian 98 output file ----------------- ... ********************************************** Gaussian 98: IBM-RS6000-G98RevA.7 11-Apr-1999 10-Jan-2001 ********************************************** %mem=6000000 ----------------------------------- #P am1 Geom=ModRedundant guess=only ----------------------------------- 1/18=150,38=1/1; 2/17=6,18=5/2; 3/5=2,11=9,12=1,25=1,30=1/1; 4/5=3,11=1,35=1/1; 6/7=3/1; 99/5=2/99; Leave Link 1 at Wed Jan 10 20:16:04 2001, MaxMem= 6000000 cpu: .2 (Enter /usr/spool/scr/aped/g98_A7_install/g98/l101.exe) --------------------- mogi + oh + methyl M4 --------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 9 fe1 1.7707 -0.62087 0.03437 fe2 -0.55637 1.04626 0.38354 o3 1.03609 0.93587 1.09577 o4 -0.20306 -0.48716 -0.8755 o5 2.15973 0.83237 -1.42382 o6 0.26517 2.17041 -1.22661 o7 0.71907 -1.78975 1.42069 o8 -1.2293 -0.53963 1.67499 c9 1.4307 1.86805 -1.7205 h10 1.84324 2.56134 -2.477 c11 -0.41795 -1.51279 1.98874 h12 -0.73053 -2.17283 2.81861 n13 3.51831 -0.92995 0.67815 h14 3.72864 -1.53685 1.47753 h15 4.33552 -0.37129 0.40979 n16 -1.1483 2.45438 1.5263 h17 -0.50694 3.26145 1.5461 h18 -1.32652 2.13513 2.49093 o19 1.84488 -2.04666 -1.5473 h20 1.22088 -1.78372 -2.25722 h21 2.69094 -2.41529 -1.87097 o22 -2.3656 1.08665 -0.85015 h23 -2.06543 0.89445 -1.76521 h24 -2.8698 1.92695 -0.78924 h25 -0.79403 -1.25645 -0.70837 c26 -3.85271 -1.85768 0.0199 h27 -3.41431 -0.85789 -0.004 h28 -4.03347 -2.48357 0.8979 f29 -4.68616 -2.16344 -1.07809 The following ModRedundant input section has been read: B 13 19 3.0000 F B 16 22 3.0000 F B 4 26 5.0000 F B 22 29 5.0000 F B 1 4 2.1775 F B 2 4 2.0153 F B 4 25 .98440 F B 26 27 1.0919 F B 26 28 1.0933 F B 26 29 1.4120 F Iteration 1 RMS(Cart)= .06157751 RMS(Int)= .20997641 Iteration 2 RMS(Cart)= .08056221 RMS(Int)= .18596981 Iteration 3 RMS(Cart)= .10116863 RMS(Int)= .16599971 Iteration 4 RMS(Cart)= .02333073 RMS(Int)= .16415597 Iteration 5 RMS(Cart)= .01049428 RMS(Int)= .16351555 Iteration 6 RMS(Cart)= .00691695 RMS(Int)= .16314443 Iteration 7 RMS(Cart)= .00515480 RMS(Int)= .16289177 Iteration 8 RMS(Cart)= .00410943 RMS(Int)= .16270408 Iteration 9 RMS(Cart)= .00342326 RMS(Int)= .16255661 Iteration 10 RMS(Cart)= .00294288 RMS(Int)= .16243603 Iteration 11 RMS(Cart)= .00259126 RMS(Int)= .16233446 Iteration 12 RMS(Cart)= .00232549 RMS(Int)= .16224687 Iteration 13 RMS(Cart)= .00211980 RMS(Int)= .16216990 Iteration 14 RMS(Cart)= .00195781 RMS(Int)= .16210117 Iteration 15 RMS(Cart)= .00182864 RMS(Int)= .16203899 Iteration 16 RMS(Cart)= .00172479 RMS(Int)= .16198208 Iteration 17 RMS(Cart)= .00164094 RMS(Int)= .16192948 Iteration 18 RMS(Cart)= .00157324 RMS(Int)= .16188044 Iteration 19 RMS(Cart)= .00151883 RMS(Int)= .16183435 Iteration 20 RMS(Cart)= .00147553 RMS(Int)= .16179073 Iteration 21 RMS(Cart)= .00144170 RMS(Int)= .16174920 Iteration 22 RMS(Cart)= .00141605 RMS(Int)= .16170944 Iteration 23 RMS(Cart)= .00139758 RMS(Int)= .16167117 Iteration 24 RMS(Cart)= .00138548 RMS(Int)= .16163418 Iteration 25 RMS(Cart)= .00137909 RMS(Int)= .16159827 Iteration 26 RMS(Cart)= .00137789 RMS(Int)= .16156328 Iteration 27 RMS(Cart)= .00138142 RMS(Int)= .16152907 Iteration 28 RMS(Cart)= .00138928 RMS(Int)= .16149554 Iteration 29 RMS(Cart)= .00140112 RMS(Int)= .16146257 Iteration 30 RMS(Cart)= .00141660 RMS(Int)= .16143010 Iteration 31 RMS(Cart)= .00143534 RMS(Int)= .16139805 Iteration 32 RMS(Cart)= .00145697 RMS(Int)= .16136637 Iteration 33 RMS(Cart)= .00148105 RMS(Int)= .16133503 Iteration 34 RMS(Cart)= .00150707 RMS(Int)= .16130400 Iteration 35 RMS(Cart)= .00153443 RMS(Int)= .16127326 Iteration 36 RMS(Cart)= .00156238 RMS(Int)= .16124283 Iteration 37 RMS(Cart)= .00159008 RMS(Int)= .16121271 Iteration 38 RMS(Cart)= .00161648 RMS(Int)= .16118294 Iteration 39 RMS(Cart)= .00164039 RMS(Int)= .16115356 Iteration 40 RMS(Cart)= .00166044 RMS(Int)= .16112462 Iteration 41 RMS(Cart)= .00167512 RMS(Int)= .16109620 Iteration 42 RMS(Cart)= .00168282 RMS(Int)= .16106837 Iteration 43 RMS(Cart)= .00168191 RMS(Int)= .16104123 Iteration 44 RMS(Cart)= .00167084 RMS(Int)= .16101488 Iteration 45 RMS(Cart)= .00164828 RMS(Int)= .16098941 Iteration 46 RMS(Cart)= .00161329 RMS(Int)= .16096493 Iteration 47 RMS(Cart)= .00156546 RMS(Int)= .16094155 Iteration 48 RMS(Cart)= .00150497 RMS(Int)= .16091935 Iteration 49 RMS(Cart)= .00143276 RMS(Int)= .16089842 Iteration 50 RMS(Cart)= .00135037 RMS(Int)= .16087884 Iteration 51 RMS(Cart)= .00125992 RMS(Int)= .16086064 Iteration 52 RMS(Cart)= .00116391 RMS(Int)= .16084387 Iteration 53 RMS(Cart)= .00106497 RMS(Int)= .16082852 Iteration 54 RMS(Cart)= .00096568 RMS(Int)= .16081459 Iteration 55 RMS(Cart)= .00086832 RMS(Int)= .16080202 Iteration 56 RMS(Cart)= .00077482 RMS(Int)= .16079076 Iteration 57 RMS(Cart)= .00068663 RMS(Int)= .16078075 Iteration 58 RMS(Cart)= .00060476 RMS(Int)= .16077189 Iteration 59 RMS(Cart)= .00052979 RMS(Int)= .16076409 Iteration 60 RMS(Cart)= .00046192 RMS(Int)= .16075727 Iteration 61 RMS(Cart)= .00040112 RMS(Int)= .16075132 Iteration 62 RMS(Cart)= .00034708 RMS(Int)= .16074615 Iteration 63 RMS(Cart)= .00029942 RMS(Int)= .16074167 Iteration 64 RMS(Cart)= .00025764 RMS(Int)= .16073781 Iteration 65 RMS(Cart)= .00022120 RMS(Int)= .16073449 Iteration 66 RMS(Cart)= .00018956 RMS(Int)= .16073163 Iteration 67 RMS(Cart)= .00016218 RMS(Int)= .16072918 Iteration 68 RMS(Cart)= .00013857 RMS(Int)= .16072708 Iteration 69 RMS(Cart)= .00011826 RMS(Int)= .16072529 Iteration 70 RMS(Cart)= .00010083 RMS(Int)= .16072376 Iteration 71 RMS(Cart)= .00008589 RMS(Int)= .16072246 Iteration 72 RMS(Cart)= .00007312 RMS(Int)= .16072134 Iteration 73 RMS(Cart)= .00006221 RMS(Int)= .16072040 Iteration 74 RMS(Cart)= .00005290 RMS(Int)= .16071959 Iteration 75 RMS(Cart)= .00004496 RMS(Int)= .16071890 Iteration 76 RMS(Cart)= .00003820 RMS(Int)= .16071832 Iteration 77 RMS(Cart)= .00003245 RMS(Int)= .16071783 Iteration 78 RMS(Cart)= .00002755 RMS(Int)= .16071741 Iteration 79 RMS(Cart)= .00002339 RMS(Int)= .16071705 Iteration 80 RMS(Cart)= .00001986 RMS(Int)= .16071674 Iteration 81 RMS(Cart)= .00001685 RMS(Int)= .16071649 Iteration 82 RMS(Cart)= .00001430 RMS(Int)= .16071627 Iteration 83 RMS(Cart)= .00001209 RMS(Int)= .16071608 Iteration 84 RMS(Cart)= .00001027 RMS(Int)= .16071593 Iteration 85 RMS(Cart)= .00000872 RMS(Int)= .16071579 Iteration 86 RMS(Cart)= .00000740 RMS(Int)= .16071568 Iteration 87 RMS(Cart)= .00000628 RMS(Int)= .16071558 Iteration 88 RMS(Cart)= .00000533 RMS(Int)= .16071550 Iteration 89 RMS(Cart)= .00000453 RMS(Int)= .16071543 Iteration 90 RMS(Cart)= .00000384 RMS(Int)= .16071537 Iteration 91 RMS(Cart)= .00000326 RMS(Int)= .16071532 Iteration 92 RMS(Cart)= .00000276 RMS(Int)= .16071528 Iteration 93 RMS(Cart)= .00000234 RMS(Int)= .16071525 Iteration 94 RMS(Cart)= .00000199 RMS(Int)= .16071522 Iteration 95 RMS(Cart)= .00000169 RMS(Int)= .16071519 Iteration 96 RMS(Cart)= .00000143 RMS(Int)= .16071517 Iteration 97 RMS(Cart)= .00000121 RMS(Int)= .16071515 Iteration 98 RMS(Cart)= .00000103 RMS(Int)= .16071513 Iteration 99 RMS(Cart)= .00000087 RMS(Int)= .16071512 Iteration 1 RMS(Cart)= .16300992 RMS(Int)= .15822705 Iteration 2 RMS(Cart)= .02939467 RMS(Int)= .15442821 Iteration 3 RMS(Cart)= .05018470 RMS(Int)= .14769850 Iteration 4 RMS(Cart)= .04621838 RMS(Int)= .14193827 Iteration 5 RMS(Cart)= .01293898 RMS(Int)= .14066646 Iteration 6 RMS(Cart)= .00383491 RMS(Int)= .14032527 Iteration 7 RMS(Cart)= .00141483 RMS(Int)= .14020347 Iteration 8 RMS(Cart)= .00056004 RMS(Int)= .14015586 Iteration 9 RMS(Cart)= .00022761 RMS(Int)= .14013661 Iteration 10 RMS(Cart)= .00009358 RMS(Int)= .14012871 Iteration 11 RMS(Cart)= .00003849 RMS(Int)= .14012546 Iteration 12 RMS(Cart)= .00001604 RMS(Int)= .14012411 Iteration 13 RMS(Cart)= .00000661 RMS(Int)= .14012355 Iteration 14 RMS(Cart)= .00000273 RMS(Int)= .14012332 Iteration 15 RMS(Cart)= .00000113 RMS(Int)= .14012323 Iteration 16 RMS(Cart)= .00000047 RMS(Int)= .14012319 Fast transformation storage of 1 MWords has been initialized. Leave Link 101 at Wed Jan 10 20:16:04 2001, MaxMem= 6000000 cpu: .6 (Enter /usr/spool/scr/aped/g98_A7_install/g98/l202.exe) Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 26 0 1.852141 -.622517 .010062 2 26 0 -.580787 .896374 .321787 3 8 0 .974568 .826330 1.117956 4 8 0 -.073910 -.536562 -1.003223 5 8 0 2.240646 .936925 -1.335676 6 8 0 .265607 2.159822 -1.169786 7 8 0 .791088 -1.928891 1.262499 8 8 0 -1.235947 -.799996 1.477014 9 6 0 1.472478 1.949882 -1.612586 10 1 0 1.887546 2.709529 -2.302096 11 6 0 -.390005 -1.747284 1.779483 12 1 0 -.711237 -2.473018 2.549932 13 7 0 3.577236 -.879086 .734426 14 1 0 3.776517 -1.522616 1.507782 15 1 0 4.376561 -.262640 .547017 16 7 0 -1.313140 2.199451 1.509691 17 1 0 -.719303 3.037077 1.614291 18 1 0 -1.526841 1.812498 2.442430 19 8 0 2.092762 -1.943470 -1.646891 20 1 0 1.494998 -1.670380 -2.375503 21 1 0 2.975199 -2.246791 -1.942320 22 8 0 -2.319840 .917741 -1.010590 23 1 0 -1.959189 .798109 -1.917095 24 1 0 -2.872676 1.725670 -.929307 25 1 0 -.629987 -1.344772 -.916259 26 6 0 -4.158119 -1.351129 .393397 27 1 0 -3.305384 -1.128839 -.342645 28 1 0 -4.755406 -.597674 1.110231 29 9 0 -4.862184 -2.566259 -.004687 --------------------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 Fe .000000 2 Fe 2.885020 .000000 3 O 2.024035 1.748692 .000000 4 O 2.178028 2.016403 2.730601 .000000 5 O 2.096141 3.272509 2.763240 2.763849 .000000 6 O 3.413289 2.130135 2.741275 2.722774 2.328900 7 O 2.097867 3.278583 2.765105 2.796480 4.130937 8 O 3.423409 2.154403 2.767713 2.751599 4.797376 9 C 3.065023 3.011242 2.994352 2.990827 1.301093 10 H 4.055843 4.032984 4.009578 4.008926 2.049578 11 C 3.069718 3.024930 2.987167 3.051100 4.881549 12 H 4.055391 4.041590 3.972177 4.096456 5.953089 13 N 1.888514 4.540010 3.135190 4.058031 3.060996 14 H 2.599339 5.122909 3.677013 4.701408 4.061219 15 H 2.605864 5.096012 3.617372 4.720696 3.089599 16 N 4.497932 1.909311 2.696762 3.916145 4.724350 17 H 4.751684 2.504469 2.828949 4.476473 4.676991 18 H 4.823198 2.496284 2.997301 4.416064 5.406910 19 O 2.132677 4.369013 4.070200 2.662361 2.900932 20 H 2.629922 4.262919 4.325351 2.372798 2.904354 21 H 2.776927 5.258394 4.776179 3.619925 3.323197 22 O 4.562844 2.190888 3.923288 2.675678 4.572098 23 H 4.500928 2.631015 4.221287 2.484107 4.242161 24 H 5.359131 2.739657 4.449875 3.599478 5.189732 25 H 2.746031 2.560843 3.380283 .984880 3.690879 26 C 6.066386 4.225364 5.622348 4.392587 7.012067 27 H 5.194307 3.459246 4.926868 3.351056 6.000995 28 H 6.698556 4.503472 5.904274 5.136810 7.568500 29 F 6.990029 5.516046 6.843805 5.295687 8.030817 6 7 8 9 10 6 O .000000 7 O 4.786410 .000000 8 O 4.245083 2.330084 .000000 9 C 1.302568 4.875992 4.943989 .000000 10 H 2.053044 5.951765 6.029481 1.106692 .000000 11 C 4.938977 1.302011 1.305550 5.352010 6.458305 12 H 6.021107 2.051959 2.055596 6.454240 7.560068 13 N 4.881380 3.023834 4.870772 4.235745 4.995366 14 H 5.749452 3.022914 5.064377 5.206105 5.999536 15 H 5.071062 4.017950 5.714358 4.241796 4.811074 16 N 3.110243 4.640268 3.000618 4.191726 5.003427 17 H 3.080700 5.202488 3.874132 4.049523 4.716040 18 H 4.047421 4.556647 2.800317 5.045587 5.913817 19 O 4.516982 3.187338 4.706019 3.942603 4.703383 20 H 4.199476 3.714483 4.801824 3.699844 4.398078 21 H 5.230386 3.891307 5.614162 4.469783 5.086998 22 O 2.872741 4.790420 3.211482 3.976102 4.751903 23 H 2.713383 5.011025 3.820601 3.632581 4.312670 24 H 3.177285 5.619875 3.853343 4.404260 5.050964 25 H 3.626092 2.666015 2.528186 3.969884 4.969495 26 C 5.860006 5.058042 3.164974 6.828196 7.765609 27 H 4.924574 4.471873 2.775223 5.824022 6.748262 28 H 6.165454 5.706042 3.544299 7.258809 8.167641 29 F 7.070186 5.828506 4.297059 7.944105 8.869660 11 12 13 14 15 11 C .000000 12 H 1.106106 .000000 13 N 4.193437 4.922162 .000000 14 H 4.181411 4.704176 1.025632 .000000 15 H 5.142304 5.897721 1.026668 1.694302 .000000 16 N 4.062227 4.824557 5.830455 6.305426 6.273860 17 H 4.798525 5.588974 5.879689 6.404259 6.164011 18 H 3.795254 4.363762 6.017766 6.334206 6.538268 19 O 4.235877 5.075052 3.001208 3.600571 3.585270 20 H 4.563229 5.456337 3.825379 4.506336 4.338924 21 H 5.042412 5.815610 3.065622 3.615210 3.478142 22 O 4.314062 5.173216 6.406963 7.033001 6.975759 23 H 4.754582 5.675560 6.363612 7.072048 6.880317 24 H 5.055948 5.865654 7.152211 7.791183 7.660570 25 H 2.736171 3.646096 4.543386 5.032383 5.327073 26 C 4.034458 4.217852 7.757244 8.014344 8.605182 27 H 3.658597 4.111376 6.970862 7.330243 7.781650 28 H 4.563576 4.684544 8.345858 8.591116 9.155450 29 F 4.884093 4.874949 8.638093 8.831982 9.537580 16 17 18 19 20 16 N .000000 17 H 1.032086 .000000 18 H 1.032184 1.684496 .000000 19 O 6.223181 6.583986 6.628075 .000000 20 H 6.160841 6.556046 6.668916 .981211 .000000 21 H 7.076391 7.363294 7.481460 .978763 1.646479 22 O 3.001340 3.734074 3.654147 5.297401 4.807738 23 H 3.758192 4.361306 4.496818 4.899752 4.270244 24 H 2.933485 3.581438 3.631449 6.215552 5.718497 25 H 4.348960 5.060856 4.696116 2.881948 2.598264 26 C 4.684724 5.707223 4.596814 6.602057 6.302893 27 H 4.298569 5.279419 4.423949 5.612901 5.241130 28 H 4.453389 5.454871 4.243503 7.504018 7.236614 29 F 6.131969 7.154154 6.023820 7.173281 6.843765 21 22 23 24 25 21 H .000000 22 O 6.238575 .000000 23 H 5.798296 .982920 .000000 24 H 7.141728 .982336 1.634183 .000000 25 H 3.855361 2.825503 2.713004 3.802294 .000000 26 C 7.559233 3.240096 3.846153 3.587283 3.763370 27 H 6.576816 2.367686 2.829181 2.946121 2.744706 28 H 8.473482 3.567400 4.351062 3.619711 4.656597 29 F 8.079669 4.428725 4.837732 4.820136 4.498275 26 27 28 29 26 C .000000 27 H 1.148184 .000000 28 H 1.199290 2.120270 .000000 29 F 1.459698 2.145697 2.264899 .000000 ... Standard orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 26 0 -1.735737 -.737997 -.026121 2 26 0 .535607 .994753 -.428503 3 8 0 -.889577 .549533 -1.338751 4 8 0 .025748 -.181657 1.127769 5 8 0 -2.459853 1.003144 .889244 6 8 0 -.625885 2.418344 .649364 7 8 0 -.388106 -2.123821 -.841247 8 8 0 1.513580 -.802874 -1.101972 9 6 0 -1.848637 2.145772 1.006109 10 1 0 -2.428296 2.970657 1.462537 11 6 0 .821709 -1.897790 -1.266087 12 1 0 1.315358 -2.719544 -1.817904 13 7 0 -3.316871 -1.371551 -.841663 14 1 0 -3.345051 -2.184471 -1.466394 15 1 0 -4.196240 -.842921 -.877851 16 7 0 1.264695 2.104715 -1.800320 17 1 0 .600531 2.813636 -2.148914 18 1 0 1.635655 1.562273 -2.596278 19 8 0 -2.037308 -1.700142 1.853146 20 1 0 -1.569964 -1.201614 2.557301 21 1 0 -2.911339 -2.050467 2.120203 22 8 0 2.079514 1.530614 1.030673 23 1 0 1.622576 1.557247 1.900518 24 1 0 2.546173 2.370220 .825067 25 1 0 .673652 -.907562 1.280314 26 6 0 4.318167 -.714306 .362102 27 1 0 3.360095 -.458863 .941042 28 1 0 4.914902 -.055405 -.442916 29 9 0 5.095358 -1.712017 1.090982 --------------------------------------------------------------------- ... ------------------------ Gaussian94 input file ------------------------ Just replace the "root card" by - #P am1 opt=(AddRedundant,maxcyc=1) ------------------- (part of) Gaussian 94 output file ----------------- ... ********************************************** Gaussian 94: IBM-RS6000-G94RevC.2 5-Aug-1995 11-Jan-1901 ********************************************** %mem=6000000 ---------------------------------- #P am1 opt=(AddRedundant,maxcyc=1) ---------------------------------- 1/6=1,14=-1,18=120,26=3,38=1/1,3; 2/9=110,12=2,17=6,18=5/2; 3/5=2,11=9,12=1,25=1,30=1/1; 4/5=3,11=1,20=5,22=1,24=1,35=1/1,2; 6/7=2,8=2,9=2,10=2/1; 7//16; 1/6=1,14=-1/3(1); 99//99; 2/9=110/2; 3/5=2,11=9,12=1,25=1,30=1/1; 4/5=5,11=1,16=2,20=5,22=1,24=1,35=1/1,2; 7//16; 1/6=1,14=-1/3(-4); 6/7=2,8=2,9=2,10=2/1; 99//99; Leave Link 1 at Thu Jan 11 16:44:33 2001, MaxMem= 6000000 cpu: .1 (Enter /private/chem/g94c/l101.exe) --------------------- mogi + oh + methyl M4 --------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 9 fe1 1.7707 -0.62087 0.03437 fe2 -0.55637 1.04626 0.38354 o3 1.03609 0.93587 1.09577 o4 -0.20306 -0.48716 -0.8755 o5 2.15973 0.83237 -1.42382 o6 0.26517 2.17041 -1.22661 o7 0.71907 -1.78975 1.42069 o8 -1.2293 -0.53963 1.67499 c9 1.4307 1.86805 -1.7205 h10 1.84324 2.56134 -2.477 c11 -0.41795 -1.51279 1.98874 h12 -0.73053 -2.17283 2.81861 n13 3.51831 -0.92995 0.67815 h14 3.72864 -1.53685 1.47753 h15 4.33552 -0.37129 0.40979 n16 -1.1483 2.45438 1.5263 h17 -0.50694 3.26145 1.5461 h18 -1.32652 2.13513 2.49093 o19 1.84488 -2.04666 -1.5473 h20 1.22088 -1.78372 -2.25722 h21 2.69094 -2.41529 -1.87097 o22 -2.3656 1.08665 -0.85015 h23 -2.06543 0.89445 -1.76521 h24 -2.8698 1.92695 -0.78924 h25 -0.79403 -1.25645 -0.70837 c26 -3.85271 -1.85768 0.0199 h27 -3.41431 -0.85789 -0.004 h28 -4.03347 -2.48357 0.8979 f29 -4.68616 -2.16344 -1.07809 Adding R( 19, 13) Coordinate has been modified. New value = 3.0000 Adding R( 22, 16) Coordinate has been modified. New value = 3.0000 Adding R( 26, 4) Coordinate has been modified. New value = 5.0000 Adding R( 29, 22) Coordinate has been modified. New value = 5.0000 Adding R( 4, 1) Coordinate has been modified. New value = 2.1775 Adding R( 4, 2) Coordinate has been modified. New value = 2.0153 Adding R( 25, 4) Coordinate has been modified. New value = .9844 Adding R( 27, 26) Coordinate has been modified. New value = 1.0919 Adding R( 28, 26) Coordinate has been modified. New value = 1.0933 Adding R( 29, 26) Coordinate has been modified. New value = 1.4120 Iteration 1 RMS(Cart)= .22729320 RMS(Int)= .10767731 Iteration 2 RMS(Cart)= .05558828 RMS(Int)= .26808782 Iteration 3 RMS(Cart)= .08661520 RMS(Int)= .30190727 Iteration 4 RMS(Cart)= .15574557 RMS(Int)= .38740670 Iteration 5 RMS(Cart)= .14628695 RMS(Int)= .37257260 Iteration 6 RMS(Cart)= .27458364 RMS(Int)= .44915492 Iteration 7 RMS(Cart)= 1.04083293 RMS(Int)= .96625468 Iteration 8 RMS(Cart)= 1.21539002 RMS(Int)= 1.46983193 Iteration 9 RMS(Cart)= 1.73996847 RMS(Int)= 3.03220159 Iteration 10 RMS(Cart)= 3.29876934 RMS(Int)= 6.24819307 Iteration 11 RMS(Cart)= 6.42743713 RMS(Int)= 12.77677873 Iteration 12 RMS(Cart)= 13.09876228 RMS(Int)= 26.42467732 Iteration 13 RMS(Cart)= 26.53815050 RMS(Int)= 54.19278502 Iteration 14 RMS(Cart)= 54.30002557 RMS(Int)=111.04085290 Iteration 15 RMS(Cart)=112.19968983 RMS(Int)=228.04363931 Iteration 16 RMS(Cart)=232.60717396 RMS(Int)=468.50477797 Iteration 17 RMS(Cart)=482.51850875 RMS(Int)=962.37800598 Iteration 18 RMS(Cart)=************ RMS(Int)=************ Iteration 19 RMS(Cart)=************ RMS(Int)=************ Iteration 20 RMS(Cart)=************ RMS(Int)=************ Iteration 21 RMS(Cart)=************ RMS(Int)=************ Iteration 22 RMS(Cart)=************ RMS(Int)=************ Iteration 23 RMS(Cart)=************ RMS(Int)=************ Iteration 24 RMS(Cart)=************ RMS(Int)=************ Iteration 25 RMS(Cart)=************ RMS(Int)=************ Iteration 26 RMS(Cart)=************ RMS(Int)=************ Iteration 27 RMS(Cart)=************ RMS(Int)=************ Iteration 28 RMS(Cart)=************ RMS(Int)=************ Iteration 29 RMS(Cart)=************ RMS(Int)=************ Iteration 30 RMS(Cart)=************ RMS(Int)=************ Iteration 31 RMS(Cart)=************ RMS(Int)=************ Iteration 32 RMS(Cart)=************ RMS(Int)=************ Iteration 33 RMS(Cart)=************ RMS(Int)=************ Iteration 34 RMS(Cart)=************ RMS(Int)=************ Iteration 35 RMS(Cart)=************ RMS(Int)=************ Iteration 36 RMS(Cart)=************ RMS(Int)=************ Iteration 37 RMS(Cart)=************ RMS(Int)=************ Iteration 38 RMS(Cart)=************ RMS(Int)=************ Iteration 39 RMS(Cart)=************ RMS(Int)=************ Iteration 40 RMS(Cart)=************ RMS(Int)=************ Iteration 41 RMS(Cart)=************ RMS(Int)=************ Iteration 42 RMS(Cart)=************ RMS(Int)=************ Iteration 43 RMS(Cart)=************ RMS(Int)=************ Iteration 44 RMS(Cart)=************ RMS(Int)=************ Iteration 45 RMS(Cart)=************ RMS(Int)=************ Iteration 46 RMS(Cart)=************ RMS(Int)=************ Iteration 47 RMS(Cart)=************ RMS(Int)=************ Iteration 48 RMS(Cart)=************ RMS(Int)=************ Iteration 49 RMS(Cart)=************ RMS(Int)=************ Iteration 50 RMS(Cart)=************ RMS(Int)=************ Iteration 51 RMS(Cart)=************ RMS(Int)=************ Iteration 52 RMS(Cart)=************ RMS(Int)=************ Iteration 53 RMS(Cart)=************ RMS(Int)=************ Iteration 54 RMS(Cart)=************ RMS(Int)=************ Iteration 55 RMS(Cart)=************ RMS(Int)=************ Iteration 56 RMS(Cart)=************ RMS(Int)=************ Iteration 57 RMS(Cart)=************ RMS(Int)=************ Iteration 58 RMS(Cart)=************ RMS(Int)=************ Iteration 59 RMS(Cart)=************ RMS(Int)=************ Iteration 60 RMS(Cart)=************ RMS(Int)=************ Iteration 61 RMS(Cart)=************ RMS(Int)=************ Iteration 62 RMS(Cart)=************ RMS(Int)=************ Iteration 63 RMS(Cart)=************ RMS(Int)=************ Iteration 64 RMS(Cart)=************ RMS(Int)=************ Iteration 65 RMS(Cart)=************ RMS(Int)=************ Iteration 66 RMS(Cart)=************ RMS(Int)=************ Iteration 67 RMS(Cart)=************ RMS(Int)=************ Iteration 68 RMS(Cart)=************ RMS(Int)=************ Iteration 69 RMS(Cart)=************ RMS(Int)=************ Iteration 70 RMS(Cart)=************ RMS(Int)=************ Iteration 71 RMS(Cart)=************ RMS(Int)=************ Iteration 72 RMS(Cart)=************ RMS(Int)=************ Iteration 73 RMS(Cart)=************ RMS(Int)=************ Iteration 74 RMS(Cart)=************ RMS(Int)=************ Iteration 75 RMS(Cart)=************ RMS(Int)=************ Iteration 76 RMS(Cart)=************ RMS(Int)=************ Iteration 77 RMS(Cart)=************ RMS(Int)=************ Iteration 78 RMS(Cart)=************ RMS(Int)=************ Iteration 79 RMS(Cart)=************ RMS(Int)=************ Iteration 80 RMS(Cart)=************ RMS(Int)=************ Iteration 81 RMS(Cart)=************ RMS(Int)=************ Iteration 82 RMS(Cart)=************ RMS(Int)=************ Iteration 83 RMS(Cart)=************ RMS(Int)=************ Iteration 84 RMS(Cart)=************ RMS(Int)=************ Iteration 85 RMS(Cart)=************ RMS(Int)=************ Iteration 86 RMS(Cart)=************ RMS(Int)=************ Iteration 87 RMS(Cart)=************ RMS(Int)=************ Iteration 88 RMS(Cart)=************ RMS(Int)=************ Iteration 89 RMS(Cart)=************ RMS(Int)=************ Iteration 90 RMS(Cart)=************ RMS(Int)=************ Iteration 91 RMS(Cart)=************ RMS(Int)=************ Iteration 92 RMS(Cart)=************ RMS(Int)=************ Iteration 93 RMS(Cart)=************ RMS(Int)=************ Iteration 94 RMS(Cart)=************ RMS(Int)=************ Iteration 95 RMS(Cart)=************ RMS(Int)=************ Iteration 96 RMS(Cart)=************ RMS(Int)=************ Iteration 97 RMS(Cart)=************ RMS(Int)=************ Iteration 98 RMS(Cart)=************ RMS(Int)=************ Iteration 99 RMS(Cart)=************ RMS(Int)=************ Iteration100 RMS(Cart)=************ RMS(Int)=************ Curvilinear step not converged, using linear step Iteration 1 RMS(Cart)= .04854927 RMS(Int)= .33917107 Iteration 2 RMS(Cart)= .02387594 RMS(Int)= .34206545 Iteration 3 RMS(Cart)= .01434075 RMS(Int)= .34153076 Iteration 4 RMS(Cart)= .00918317 RMS(Int)= .34084169 Iteration 5 RMS(Cart)= .00603757 RMS(Int)= .34030396 Iteration 6 RMS(Cart)= .00402700 RMS(Int)= .33991659 Iteration 7 RMS(Cart)= .00271042 RMS(Int)= .33964440 Iteration 8 RMS(Cart)= .00183522 RMS(Int)= .33945518 Iteration 9 RMS(Cart)= .00124761 RMS(Int)= .33932436 Iteration 10 RMS(Cart)= .00085043 RMS(Int)= .33923419 Iteration 11 RMS(Cart)= .00058075 RMS(Int)= .33917216 Iteration 12 RMS(Cart)= .00039708 RMS(Int)= .33912954 Iteration 13 RMS(Cart)= .00027173 RMS(Int)= .33910028 Iteration 14 RMS(Cart)= .00018605 RMS(Int)= .33908019 Iteration 15 RMS(Cart)= .00012744 RMS(Int)= .33906642 Iteration 16 RMS(Cart)= .00008732 RMS(Int)= .33905696 Iteration 17 RMS(Cart)= .00005984 RMS(Int)= .33905048 Iteration 18 RMS(Cart)= .00004101 RMS(Int)= .33904604 Iteration 19 RMS(Cart)= .00002811 RMS(Int)= .33904299 Iteration 20 RMS(Cart)= .00001927 RMS(Int)= .33904090 Iteration 21 RMS(Cart)= .00001321 RMS(Int)= .33903947 Iteration 22 RMS(Cart)= .00000905 RMS(Int)= .33903849 Leave Link 101 at Thu Jan 11 16:44:37 2001, MaxMem= 6000000 cpu: 3.4 (Enter /private/chem/g94c/l103.exe) GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Initialization pass. ---------------------------- ! Initial Parameters ! ! (Angstroms and Degrees) ! ------------------------ ------------------------- ! Name Definition Value Derivative Info. ! ----------------------------------------------------------------------------- ! R1 R(2,1) 2.906 estimate D2E/DX2 ! ! R2 R(3,1) 2.0142 estimate D2E/DX2 ! ! R3 R(3,2) 1.7551 estimate D2E/DX2 ! ! R4 R(4,1) 2.1775 Frozen ! ! R5 R(4,2) 2.0153 Frozen ! ! R6 R(5,1) 2.0968 estimate D2E/DX2 ! ! R7 R(6,2) 2.1312 estimate D2E/DX2 ! ! R8 R(7,1) 2.1009 estimate D2E/DX2 ! ! R9 R(8,2) 2.1546 estimate D2E/DX2 ! ! R10 R(9,5) 1.3038 estimate D2E/DX2 ! ! R11 R(9,6) 1.3064 estimate D2E/DX2 ! ! R12 R(10,9) 1.1072 estimate D2E/DX2 ! ! R13 R(11,7) 1.3089 estimate D2E/DX2 ! ! R14 R(11,8) 1.311 estimate D2E/DX2 ! ! R15 R(12,11) 1.1064 estimate D2E/DX2 ! ! R16 R(13,1) 1.8891 estimate D2E/DX2 ! ! R17 R(14,13) 1.0256 estimate D2E/DX2 ! ! R18 R(15,13) 1.0282 estimate D2E/DX2 ! ! R19 R(16,2) 1.9131 estimate D2E/DX2 ! ! R20 R(17,16) 1.0329 estimate D2E/DX2 ! ! R21 R(18,16) 1.0323 estimate D2E/DX2 ! ! R22 R(19,1) 2.1349 estimate D2E/DX2 ! ! R23 R(20,19) 0.9815 estimate D2E/DX2 ! ! R24 R(21,19) 0.9805 estimate D2E/DX2 ! ! R25 R(22,2) 2.2396 estimate D2E/DX2 ! ! R26 R(23,22) 0.9836 estimate D2E/DX2 ! ! R27 R(24,22) 0.9862 estimate D2E/DX2 ! ! R28 R(25,4) 0.9844 Frozen ! ! R29 R(27,22) 2.6621 estimate D2E/DX2 ! ! R30 R(27,26) 1.0919 Frozen ! ! R31 R(28,26) 1.0933 Frozen ! ! R32 R(29,26) 1.412 Frozen ! ! R33 R(19,13) 3. Frozen ! ! R34 R(22,16) 3. Frozen ! ! R35 R(26,4) 5. Frozen ! ! R36 R(29,22) 5. Frozen ! ! A1 A(2,1,3) 36.4084 estimate D2E/DX2 ! ! A2 A(1,2,3) 42.9361 estimate D2E/DX2 ! ! A3 A(1,3,2) 100.6555 estimate D2E/DX2 ! ! A4 A(2,1,4) 43.8623 estimate D2E/DX2 ! ! A5 A(3,1,4) 80.269 estimate D2E/DX2 ! ! A6 A(1,2,4) 48.4776 estimate D2E/DX2 ! ! A7 A(3,2,4) 91.4118 estimate D2E/DX2 ! ! A8 A(1,4,2) 87.6601 estimate D2E/DX2 ! ! A9 A(2,1,5) 80.3398 estimate D2E/DX2 ! ! A10 A(3,1,5) 84.3149 estimate D2E/DX2 ! ! A11 A(4,1,5) 80.1553 estimate D2E/DX2 ! ! A12 A(1,2,6) 84.1333 estimate D2E/DX2 ! ! A13 A(3,2,6) 89.332 estimate D2E/DX2 ! ! A14 A(4,2,6) 81.6127 estimate D2E/DX2 ! ! A15 A(2,1,7) 80.2566 estimate D2E/DX2 ! ! A16 A(3,1,7) 83.7987 estimate D2E/DX2 ! ! A17 A(4,1,7) 81.5506 estimate D2E/DX2 ! ! A18 A(5,1,7) 159.6124 estimate D2E/DX2 ! ! A19 A(1,2,8) 84.4762 estimate D2E/DX2 ! ! A20 A(3,2,8) 89.5125 estimate D2E/DX2 ! ! A21 A(4,2,8) 82.9214 estimate D2E/DX2 ! ! A22 A(6,2,8) 164.4571 estimate D2E/DX2 ! ! A23 A(1,5,9) 127.3071 estimate D2E/DX2 ! ! A24 A(2,6,9) 120.7722 estimate D2E/DX2 ! ! A25 A(5,9,6) 127.1868 estimate D2E/DX2 ! ! A26 A(5,9,10) 116.2603 estimate D2E/DX2 ! ! A27 A(6,9,10) 116.5528 estimate D2E/DX2 ! ! A28 A(1,7,11) 127.6332 estimate D2E/DX2 ! ! A29 A(2,8,11) 119.5157 estimate D2E/DX2 ! ! A30 A(7,11,8) 127.1267 estimate D2E/DX2 ! ! A31 A(7,11,12) 116.4483 estimate D2E/DX2 ! ! A32 A(8,11,12) 116.425 estimate D2E/DX2 ! ! A33 A(2,1,13) 143.1571 estimate D2E/DX2 ! ! A34 A(3,1,13) 106.7534 estimate D2E/DX2 ! ! A35 A(4,1,13) 172.9723 estimate D2E/DX2 ! ! A36 A(5,1,13) 100.5447 estimate D2E/DX2 ! ! A37 A(7,1,13) 98.7157 estimate D2E/DX2 ! ! A38 A(1,13,14) 123.4448 estimate D2E/DX2 ! ! A39 A(1,13,15) 124.0997 estimate D2E/DX2 ! ! A40 A(14,13,15) 111.2745 estimate D2E/DX2 ! ! A41 A(1,2,16) 137.8825 estimate D2E/DX2 ! ! A42 A(3,2,16) 95.0101 estimate D2E/DX2 ! ! A43 A(4,2,16) 173.2176 estimate D2E/DX2 ! ! A44 A(6,2,16) 100.6087 estimate D2E/DX2 ! ! A45 A(8,2,16) 94.9329 estimate D2E/DX2 ! ! A46 A(2,16,17) 113.35 estimate D2E/DX2 ! ! A47 A(2,16,18) 112.6919 estimate D2E/DX2 ! ! A48 A(17,16,18) 109.3844 estimate D2E/DX2 ! ! A49 A(2,1,19) 120.5042 estimate D2E/DX2 ! ! A50 A(3,1,19) 156.4578 estimate D2E/DX2 ! ! A51 A(4,1,19) 76.8147 estimate D2E/DX2 ! ! A52 A(5,1,19) 86.5273 estimate D2E/DX2 ! ! A53 A(7,1,19) 97.9971 estimate D2E/DX2 ! ! A54 A(13,1,19) 96.2183 estimate D2E/DX2 ! ! A55 A(1,19,20) 109.6042 estimate D2E/DX2 ! ! A56 A(1,19,21) 121.9011 estimate D2E/DX2 ! ! A57 A(20,19,21) 114.299 estimate D2E/DX2 ! ! A58 A(1,2,22) 129.9188 estimate D2E/DX2 ! ! A59 A(3,2,22) 171.369 estimate D2E/DX2 ! ! A60 A(4,2,22) 81.6246 estimate D2E/DX2 ! ! A61 A(6,2,22) 84.6312 estimate D2E/DX2 ! ! A62 A(8,2,22) 94.6495 estimate D2E/DX2 ! ! A63 A(16,2,22) 92.166 estimate D2E/DX2 ! ! A64 A(2,22,23) 104.0952 estimate D2E/DX2 ! ! A65 A(2,22,24) 108.1512 estimate D2E/DX2 ! ! A66 A(23,22,24) 114.4776 estimate D2E/DX2 ! ! A67 A(1,4,25) 114.7512 estimate D2E/DX2 ! ! A68 A(2,4,25) 112.1669 estimate D2E/DX2 ! ! A69 A(2,22,27) 114.2928 estimate D2E/DX2 ! ! A70 A(23,22,27) 105.9841 estimate D2E/DX2 ! ! A71 A(24,22,27) 109.8816 estimate D2E/DX2 ! ! A72 A(22,27,26) 164.2718 estimate D2E/DX2 ! ! A73 A(27,26,28) 117.9013 estimate D2E/DX2 ! ! A74 A(27,26,29) 140.4709 estimate D2E/DX2 ! ! A75 A(28,26,29) 101.3719 estimate D2E/DX2 ! ! D1 D(3,2,1,4) -179.3297 estimate D2E/DX2 ! ! D2 D(3,2,1,5) -93.5263 estimate D2E/DX2 ! ! D3 D(3,2,1,7) 92.7612 estimate D2E/DX2 ! ! D4 D(3,2,1,13) 1.2006 estimate D2E/DX2 ! ! D5 D(3,2,1,19) -173.6456 estimate D2E/DX2 ! ! D6 D(4,2,1,3) 179.3297 estimate D2E/DX2 ! ! D7 D(4,2,1,5) 85.8034 estimate D2E/DX2 ! ! D8 D(4,2,1,7) -87.9092 estimate D2E/DX2 ! ! D9 D(4,2,1,13) -179.4698 estimate D2E/DX2 ! ! D10 D(4,2,1,19) 5.6841 estimate D2E/DX2 ! ! D11 D(6,2,1,3) 95.3494 estimate D2E/DX2 ! ! D12 D(6,2,1,4) -83.9803 estimate D2E/DX2 ! ! D13 D(6,2,1,5) 1.8231 estimate D2E/DX2 ! ! D14 D(6,2,1,7) -171.8894 estimate D2E/DX2 ! ! D15 D(6,2,1,13) 96.55 estimate D2E/DX2 ! ! D16 D(6,2,1,19) -78.2962 estimate D2E/DX2 ! ! D17 D(8,2,1,3) -95.2436 estimate D2E/DX2 ! ! D18 D(8,2,1,4) 85.4268 estimate D2E/DX2 ! ! D19 D(8,2,1,5) 171.2301 estimate D2E/DX2 ! ! D20 D(8,2,1,7) -2.4824 estimate D2E/DX2 ! ! D21 D(8,2,1,13) -94.043 estimate D2E/DX2 ! ! D22 D(8,2,1,19) 91.1108 estimate D2E/DX2 ! ! D23 D(16,2,1,3) -3.9914 estimate D2E/DX2 ! ! D24 D(16,2,1,4) 176.6789 estimate D2E/DX2 ! ! D25 D(16,2,1,5) -97.5177 estimate D2E/DX2 ! ! D26 D(16,2,1,7) 88.7698 estimate D2E/DX2 ! ! D27 D(16,2,1,13) -2.7908 estimate D2E/DX2 ! ! D28 D(16,2,1,19) -177.637 estimate D2E/DX2 ! ! D29 D(22,2,1,3) 173.3085 estimate D2E/DX2 ! ! D30 D(22,2,1,4) -6.0212 estimate D2E/DX2 ! ! D31 D(22,2,1,5) 79.7822 estimate D2E/DX2 ! ! D32 D(22,2,1,7) -93.9303 estimate D2E/DX2 ! ! D33 D(22,2,1,13) 174.5091 estimate D2E/DX2 ! ! D34 D(22,2,1,19) -0.3371 estimate D2E/DX2 ! ! D35 D(2,3,1,4) 0.4713 estimate D2E/DX2 ! ! D36 D(2,3,1,5) 81.4234 estimate D2E/DX2 ! ! D37 D(2,3,1,7) -81.9826 estimate D2E/DX2 ! ! D38 D(2,3,1,13) -179.2482 estimate D2E/DX2 ! ! D39 D(2,3,1,19) 13.8122 estimate D2E/DX2 ! ! D40 D(1,3,2,4) -0.502 estimate D2E/DX2 ! ! D41 D(1,3,2,6) -82.0949 estimate D2E/DX2 ! ! D42 D(1,3,2,8) 82.4049 estimate D2E/DX2 ! ! D43 D(1,3,2,16) 177.3141 estimate D2E/DX2 ! ! D44 D(1,3,2,22) -36.5492 estimate D2E/DX2 ! ! D45 D(2,4,1,3) -0.4037 estimate D2E/DX2 ! ! D46 D(2,4,1,5) -86.2604 estimate D2E/DX2 ! ! D47 D(2,4,1,7) 84.7015 estimate D2E/DX2 ! ! D48 D(2,4,1,13) 177.4005 estimate D2E/DX2 ! ! D49 D(2,4,1,19) -174.9719 estimate D2E/DX2 ! ! D50 D(25,4,1,2) -113.3896 estimate D2E/DX2 ! ! D51 D(25,4,1,3) -113.7933 estimate D2E/DX2 ! ! D52 D(25,4,1,5) 160.35 estimate D2E/DX2 ! ! D53 D(25,4,1,7) -28.6881 estimate D2E/DX2 ! ! D54 D(25,4,1,13) 64.0108 estimate D2E/DX2 ! ! D55 D(25,4,1,19) 71.6385 estimate D2E/DX2 ! ! D56 D(1,4,2,3) 0.4567 estimate D2E/DX2 ! ! D57 D(1,4,2,6) 89.5731 estimate D2E/DX2 ! ! D58 D(1,4,2,8) -88.8765 estimate D2E/DX2 ! ! D59 D(1,4,2,16) -160.7931 estimate D2E/DX2 ! ! D60 D(1,4,2,22) 175.3357 estimate D2E/DX2 ! ! D61 D(25,4,2,1) 115.8377 estimate D2E/DX2 ! ! D62 D(25,4,2,3) 116.2944 estimate D2E/DX2 ! ! D63 D(25,4,2,6) -154.5893 estimate D2E/DX2 ! ! D64 D(25,4,2,8) 26.9612 estimate D2E/DX2 ! ! D65 D(25,4,2,16) -44.9555 estimate D2E/DX2 ! ! D66 D(25,4,2,22) -68.8267 estimate D2E/DX2 ! ! D67 D(9,5,1,2) 0.2339 estimate D2E/DX2 ! ! D68 D(9,5,1,3) -36.3031 estimate D2E/DX2 ! ! D69 D(9,5,1,4) 44.7731 estimate D2E/DX2 ! ! D70 D(9,5,1,7) 18.2832 estimate D2E/DX2 ! ! D71 D(9,5,1,13) -142.332 estimate D2E/DX2 ! ! D72 D(9,5,1,19) 121.9815 estimate D2E/DX2 ! ! D73 D(9,6,2,1) -4.5598 estimate D2E/DX2 ! ! D74 D(9,6,2,3) 38.1482 estimate D2E/DX2 ! ! D75 D(9,6,2,4) -53.3775 estimate D2E/DX2 ! ! D76 D(9,6,2,8) -47.6266 estimate D2E/DX2 ! ! D77 D(9,6,2,16) 133.1204 estimate D2E/DX2 ! ! D78 D(9,6,2,22) -135.6752 estimate D2E/DX2 ! ! D79 D(11,7,1,2) -2.2643 estimate D2E/DX2 ! ! D80 D(11,7,1,3) 34.3437 estimate D2E/DX2 ! ! D81 D(11,7,1,4) -46.6965 estimate D2E/DX2 ! ! D82 D(11,7,1,5) -20.3183 estimate D2E/DX2 ! ! D83 D(11,7,1,13) 140.4058 estimate D2E/DX2 ! ! D84 D(11,7,1,19) -121.9977 estimate D2E/DX2 ! ! D85 D(11,8,2,1) 7.9159 estimate D2E/DX2 ! ! D86 D(11,8,2,3) -34.7994 estimate D2E/DX2 ! ! D87 D(11,8,2,4) 56.6838 estimate D2E/DX2 ! ! D88 D(11,8,2,6) 50.9508 estimate D2E/DX2 ! ! D89 D(11,8,2,16) -129.7862 estimate D2E/DX2 ! ! D90 D(11,8,2,22) 137.6301 estimate D2E/DX2 ! ! D91 D(6,9,5,1) -4.2323 estimate D2E/DX2 ! ! D92 D(10,9,5,1) 175.8042 estimate D2E/DX2 ! ! D93 D(5,9,6,2) 6.6148 estimate D2E/DX2 ! ! D94 D(10,9,6,2) -173.4218 estimate D2E/DX2 ! ! D95 D(8,11,7,1) 10.1145 estimate D2E/DX2 ! ! D96 D(12,11,7,1) -169.8864 estimate D2E/DX2 ! ! D97 D(7,11,8,2) -12.9213 estimate D2E/DX2 ! ! D98 D(12,11,8,2) 167.0796 estimate D2E/DX2 ! ! D99 D(14,13,1,2) 86.5845 estimate D2E/DX2 ! ! D100 D(14,13,1,3) 87.3286 estimate D2E/DX2 ! ! D101 D(14,13,1,4) -90.4111 estimate D2E/DX2 ! ! D102 D(14,13,1,5) 174.5089 estimate D2E/DX2 ! ! D103 D(14,13,1,7) 1.2266 estimate D2E/DX2 ! ! D104 D(14,13,1,19) -97.8808 estimate D2E/DX2 ! ! D105 D(15,13,1,2) -79.9027 estimate D2E/DX2 ! ! D106 D(15,13,1,3) -79.1586 estimate D2E/DX2 ! ! D107 D(15,13,1,4) 103.1017 estimate D2E/DX2 ! ! D108 D(15,13,1,5) 8.0217 estimate D2E/DX2 ! ! D109 D(15,13,1,7) -165.2606 estimate D2E/DX2 ! ! D110 D(15,13,1,19) 95.632 estimate D2E/DX2 ! ! D111 D(17,16,2,1) 55.3474 estimate D2E/DX2 ! ! D112 D(17,16,2,3) 52.6193 estimate D2E/DX2 ! ! D113 D(17,16,2,4) -146.1995 estimate D2E/DX2 ! ! D114 D(17,16,2,6) -37.6393 estimate D2E/DX2 ! ! D115 D(17,16,2,8) 142.5616 estimate D2E/DX2 ! ! D116 D(17,16,2,22) -122.5806 estimate D2E/DX2 ! ! D117 D(18,16,2,1) -69.5674 estimate D2E/DX2 ! ! D118 D(18,16,2,3) -72.2955 estimate D2E/DX2 ! ! D119 D(18,16,2,4) 88.8857 estimate D2E/DX2 ! ! D120 D(18,16,2,6) -162.5541 estimate D2E/DX2 ! ! D121 D(18,16,2,8) 17.6468 estimate D2E/DX2 ! ! D122 D(18,16,2,22) 112.5046 estimate D2E/DX2 ! ! D123 D(20,19,1,2) 22.7148 estimate D2E/DX2 ! ! D124 D(20,19,1,3) 13.2486 estimate D2E/DX2 ! ! D125 D(20,19,1,4) 26.7568 estimate D2E/DX2 ! ! D126 D(20,19,1,5) -53.9369 estimate D2E/DX2 ! ! D127 D(20,19,1,7) 106.0775 estimate D2E/DX2 ! ! D128 D(20,19,1,13) -154.1793 estimate D2E/DX2 ! ! D129 D(21,19,1,2) 160.1266 estimate D2E/DX2 ! ! D130 D(21,19,1,3) 150.6605 estimate D2E/DX2 ! ! D131 D(21,19,1,4) 164.1686 estimate D2E/DX2 ! ! D132 D(21,19,1,5) 83.4749 estimate D2E/DX2 ! ! D133 D(21,19,1,7) -116.5106 estimate D2E/DX2 ! ! D134 D(21,19,1,13) -16.7674 estimate D2E/DX2 ! ! D135 D(23,22,2,1) -34.3673 estimate D2E/DX2 ! ! D136 D(23,22,2,3) -2.4353 estimate D2E/DX2 ! ! D137 D(23,22,2,4) -38.9204 estimate D2E/DX2 ! ! D138 D(23,22,2,6) 43.3644 estimate D2E/DX2 ! ! D139 D(23,22,2,8) -121.0494 estimate D2E/DX2 ! ! D140 D(23,22,2,16) 143.8209 estimate D2E/DX2 ! ! D141 D(24,22,2,1) -156.5005 estimate D2E/DX2 ! ! D142 D(24,22,2,3) -124.5685 estimate D2E/DX2 ! ! D143 D(24,22,2,4) -161.0536 estimate D2E/DX2 ! ! D144 D(24,22,2,6) -78.7688 estimate D2E/DX2 ! ! D145 D(24,22,2,8) 116.8175 estimate D2E/DX2 ! ! D146 D(24,22,2,16) 21.6877 estimate D2E/DX2 ! ! D147 D(27,22,2,1) 80.773 estimate D2E/DX2 ! ! D148 D(27,22,2,3) 112.705 estimate D2E/DX2 ! ! D149 D(27,22,2,4) 76.2199 estimate D2E/DX2 ! ! D150 D(27,22,2,6) 158.5047 estimate D2E/DX2 ! ! D151 D(27,22,2,8) -5.9091 estimate D2E/DX2 ! ! D152 D(27,22,2,16) -101.0388 estimate D2E/DX2 ! ! D153 D(26,27,22,2) 68.2005 estimate D2E/DX2 ! ! D154 D(26,27,22,23) -177.7686 estimate D2E/DX2 ! ! D155 D(26,27,22,24) -53.5809 estimate D2E/DX2 ! ! D156 D(22,27,26,28) -18.2812 estimate D2E/DX2 ! ! D157 D(22,27,26,29) 154.5667 estimate D2E/DX2 ! ----------------------------------------------------------------------------- Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-06 Number of steps in this run= 1 maximum allowed number of steps= 174. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Leave Link 103 at Thu Jan 11 16:44:38 2001, MaxMem= 6000000 cpu: .1 (Enter /private/chem/g94c/l202.exe) Input orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 26 1.958452 -.578521 .030560 2 26 -.487152 .961439 .334123 3 8 1.093401 .896998 1.094336 4 8 .013223 -.512635 -.945786 5 8 2.316097 .931384 -1.379646 6 8 .336807 2.165174 -1.219565 7 8 .909009 -1.833955 1.348232 8 8 -1.126122 -.687339 1.565160 9 6 1.537347 1.933101 -1.679508 10 1 1.939867 2.666521 -2.404691 11 6 -.269411 -1.628590 1.879634 12 1 -.576343 -2.325651 2.682189 13 7 3.695514 -.811681 .735471 14 1 3.906186 -1.428996 1.526860 15 1 4.493699 -.202230 .514937 16 7 -1.177594 2.313349 1.498490 17 1 -.574619 3.149972 1.557347 18 1 -1.367773 1.960461 2.449784 19 8 2.176848 -1.958383 -1.583738 20 1 1.566931 -1.712153 -2.312230 21 1 3.056735 -2.271183 -1.882550 22 8 -2.340449 .978098 -.923260 23 1 -2.010335 .833133 -1.838424 24 1 -2.797381 1.841197 -.785594 25 1 -.538919 -1.317725 -.819246 26 6 -4.742515 -1.701185 .039258 27 1 -4.020643 -1.025522 -.424052 28 1 -4.871017 -1.647120 1.123650 29 9 -5.736453 -2.640473 -.312406 ---------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 5 1 Fe .000000 2 Fe 2.905961 .000000 3 O 2.014222 1.755057 .000000 4 O 2.177500 2.015300 2.704801 .000000 5 O 2.096760 3.285744 2.759847 2.752571 .000000 6 O 3.423508 2.131158 2.744967 2.711147 2.337830 7 O 2.100881 3.285104 2.748921 2.794787 4.131381 8 O 3.446945 2.154577 2.767324 2.762875 4.810511 9 C 3.067558 3.016195 2.994129 2.973706 1.303766 10 H 4.057228 4.037181 4.011348 3.993419 2.050114 11 C 3.079787 3.023949 2.975322 3.050940 4.884794 12 H 4.063099 4.040585 3.961664 4.098392 5.955919 13 N 1.889086 4.560672 3.133586 4.058980 3.068352 14 H 2.599210 5.141812 3.675471 4.702006 4.067868 15 H 2.608389 5.118173 3.620225 4.722788 3.101044 16 N 4.511376 1.913144 2.706808 3.921571 4.732797 17 H 4.759116 2.508706 2.841225 4.475033 4.680203 18 H 4.833512 2.499912 3.004258 4.421905 5.412432 19 O 2.134871 4.393228 4.061914 2.679262 2.900310 20 H 2.631934 4.286086 4.317012 2.391656 2.901595 21 H 2.780525 5.284186 4.770105 3.637716 3.325340 22 O 4.670480 2.239643 3.983541 2.786138 4.679091 23 H 4.608377 2.656409 4.270636 2.588954 4.351797 24 H 5.398063 2.713834 4.423102 3.669561 5.227649 25 H 2.739608 2.554902 3.351307 .984400 3.677452 26 C 6.794365 5.028381 6.474693 5.000001 7.666009 27 H 6.012991 4.124124 5.670541 4.099676 6.700516 28 H 6.998456 5.161996 6.484418 5.424520 8.035532 29 F 7.973759 6.398979 7.819177 6.163412 8.873597 6 7 8 9 10 6 O .000000 7 O 4.786860 .000000 8 O 4.246373 2.345964 .000000 9 C 1.306407 4.873677 4.948600 .000000 10 H 2.055645 5.949906 6.033936 1.107167 .000000 11 C 4.936109 1.308907 1.311031 5.349533 6.456340 12 H 6.018723 2.056083 2.057687 6.452058 7.558402 13 N 4.895380 3.030697 4.894080 4.245426 5.004079 14 H 5.762063 3.029681 5.086811 5.214968 6.008058 15 H 5.088501 4.025780 5.737655 4.256200 4.824522 16 N 3.114994 4.645064 3.001870 4.197042 5.007806 17 H 3.084115 5.204268 3.876747 4.051963 4.717427 18 H 4.051126 4.560126 2.802106 5.048912 5.916496 19 O 4.530132 3.196771 4.737164 3.944843 4.703176 20 H 4.211981 3.721112 4.830831 3.699878 4.395500 21 H 5.245837 3.904080 5.647261 4.475016 5.089297 22 O 2.943577 4.860689 3.231177 4.064634 4.833893 23 H 2.768825 5.078455 3.831194 3.717692 4.391591 24 H 3.180633 5.638908 3.835707 4.426894 5.073870 25 H 3.613548 2.657244 2.535268 3.952063 4.953003 26 C 6.506372 5.802651 4.053956 7.456464 8.348890 27 H 5.459007 5.300569 3.528397 6.420349 7.285726 28 H 6.866270 5.787404 3.891060 7.857659 8.800275 29 F 7.797542 6.897127 5.347442 8.700271 9.563877 11 12 13 14 15 11 C .000000 12 H 1.106434 .000000 13 N 4.206789 4.932603 .000000 14 H 4.195223 4.715065 1.025552 .000000 15 H 5.155978 5.908572 1.028186 1.695322 .000000 16 N 4.063121 4.825243 5.839109 6.312747 6.281646 17 H 4.799132 5.589965 5.882534 6.406676 6.165365 18 H 3.796414 4.364760 6.021670 6.336786 6.540467 19 O 4.252986 5.090489 3.000001 3.598150 3.585570 20 H 4.577210 5.469389 3.824944 4.504542 4.340358 21 H 5.062627 5.834300 3.064673 3.613160 3.477553 22 O 4.352038 5.198662 6.510572 7.128650 7.082878 23 H 4.786946 5.698262 6.472021 7.172697 6.993764 24 H 5.053068 5.858425 7.176983 7.808932 7.682891 25 H 2.730059 3.643811 4.539124 5.027480 5.324623 26 C 4.837449 4.973131 8.513299 8.779925 9.369140 27 H 4.443243 4.816874 7.805723 8.173340 8.605436 28 H 4.663328 4.618839 8.615920 8.789167 9.495059 29 F 5.976412 5.974400 9.664602 9.890959 10.549196 16 17 18 19 20 16 N .000000 17 H 1.032947 .000000 18 H 1.032307 1.685370 .000000 19 O 6.245007 6.597900 6.647629 .000000 20 H 6.185359 6.572680 6.691588 .981493 .000000 21 H 7.097810 7.376214 7.500146 .980476 1.648227 22 O 3.000000 3.740134 3.645348 5.428179 4.943107 23 H 3.744261 4.354341 4.480232 5.038842 4.415858 24 H 2.839661 3.484671 3.539163 6.310055 5.831306 25 H 4.354825 5.060610 4.703196 2.893144 2.611356 26 C 5.563677 6.573406 5.532375 7.111810 6.733403 27 H 4.788231 5.765047 4.920645 6.373696 5.937817 28 H 5.428370 6.454395 5.200576 7.556403 7.297716 29 F 6.971578 7.979333 6.919802 8.043747 7.628924 21 22 23 24 25 21 H .000000 22 O 6.372414 .000000 23 H 5.942551 .983623 .000000 24 H 7.237793 .986245 1.656528 .000000 25 H 3.868905 2.920125 2.798210 3.883371 .000000 26 C 8.052734 3.724905 4.172920 4.124609 4.307469 27 H 7.332678 2.662095 3.081621 3.137700 3.516243 28 H 8.501525 4.181553 4.807186 4.484812 4.759245 29 F 8.939904 5.000004 5.317765 5.380281 5.387106 26 27 28 29 26 C .000000 27 H 1.091913 .000000 28 H 1.093317 1.872138 .000000 29 F 1.412035 2.358927 1.948842 .000000 Stoichiometry C3H13FFe2N2O8(9) Framework group C1[X(C3H13FFe2N2O8)] Deg. of freedom 81 Full point group C1 NOp 1 Largest Abelian subgroup C1 NOp 1 Largest concise Abelian subgroup C1 NOp 1 Standard orientation: ---------------------------------------------------------- Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------- 1 26 1.803608 -.797142 -.029008 2 26 -.388448 1.047763 .456608 3 8 1.110028 .595373 1.250421 4 8 -.040027 -.246417 -1.048429 5 8 2.482084 .853084 -1.130293 6 8 .711640 2.348732 -.823672 7 8 .488637 -2.070816 1.001673 8 8 -1.354068 -.660452 1.346430 9 6 1.889159 2.005372 -1.273398 10 1 2.446887 2.776326 -1.839427 11 6 -.675877 -1.769300 1.517650 12 1 -1.138792 -2.533900 2.169794 13 7 3.433838 -1.429598 .685833 14 1 3.494245 -2.199713 1.360393 15 1 4.329467 -.930625 .608105 16 7 -.935616 2.274290 1.819090 17 1 -.215460 2.977974 2.049707 18 1 -1.239829 1.799325 2.683683 19 8 1.910477 -1.896130 -1.856158 20 1 1.394917 -1.431803 -2.550367 21 1 2.748885 -2.292986 -2.173821 22 8 -2.130748 1.583851 -.844546 23 1 -1.768071 1.546048 -1.758083 24 1 -2.456457 2.473565 -.570682 25 1 -.717287 -.959646 -1.089258 26 6 -4.976492 -.790096 -.469002 27 1 -4.129992 -.172597 -.776263 28 1 -5.165548 -.902723 .601939 29 9 -6.078847 -1.479099 -1.020301 ---------------------------------------------------------- ... ------------------------------------------------------------------------ Dr. Pinchas Aped Tel.: (+972-3) 531-8634 Department of Chemistry FAX : (+972-3) 535-1250 Bar-Ilan University E-Mail: aped@hpc.biu.ac.il 52900 Ramat-Gan, ISRAEL WWW: http://www.biu.ac.il/~aped ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Thu Feb 8 04:08:00 2001 Received: from lx00.csrsrc.mi.cnr.it (IDENT:root@lx00.csrsrc.mi.cnr.it [155.253.3.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1897xw07037 for ; Thu, 8 Feb 2001 04:07:59 -0500 Received: from csrsrc.mi.cnr.it (IDENT:alex@pitpc7.csrsrc.mi.cnr.it [155.253.3.246]) by lx00.csrsrc.mi.cnr.it (8.9.3/8.8.7) with ESMTP id KAA09245 for ; Thu, 8 Feb 2001 10:07:59 +0100 Sender: alex@csrsrc.mi.cnr.it Message-ID: <3A825927.E1F939BA@csrsrc.mi.cnr.it> Date: Thu, 08 Feb 2001 09:30:31 +0100 From: Alessandro X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-5.0 i586) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL: Summary on Modelling of DNA-Protein interaction Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Here is a first Summary... hope to get more later. If anyone has something else to add, I will re-post a new Summary later. Meanwhile, thanks a lot to all who answered. Ale *****Original Question:***** Dear cclers, I am looking for some good reviews about DNA-Protein interaction, both on modelling and calculations. Despite some experiences on protein studies, I have no idea on DNA problems... so pratical suggestion on this topics are gratefully accepted, too. This is a "first look" search, just for getting an idea of the state of the art, so every good information could be useful. Thanks a lot. Ale *****Summary***** ----- From: Tanja van Mourik The following two papers contain some information on DNA-protein complexes: "Hydration of DNA: take 2", H.M. Berman, Current Opin. Struct. Biol. 4, 345-350 (1994) "Weakly Bound Clusters of Biological Interest", C. Desfrancois, S. Carles and P.J. Schermann, Chem. Rev. 100, 3943-3962 (2000) (paragraph 4.3) ----- From: Dr Mark J Forster Ph.D. Several programs are available for docking two macromolecules when one of them (typically the protein) is held rigid and then replaced by a grid. The Sterberg group have a code (Multidock) which allows full flexibility, see their web page http://www.bmm.icnet.uk/multidock/multidock.html The Nussinov group (ref 4) are also publishing reports on flexible docking but I am not sure if their codes are available. Their work focusses on protein-protein complexes. (1) Predictive docking of protein-protein and protein-DNA complexes. Sternberg MJ, Gabb HA, Jackson RM Curr Opin Struct Biol. 1998 Apr;8(2):250-6. Review. (2) Modelling repressor proteins docking to DNA. Aloy P, Moont G, Gabb HA, Querol E, Aviles FX, Sternberg MJ Proteins. 1998 Dec 1;33(4):535-49. (3) Monte Carlo docking of protein-DNA complexes: incorporation of DNA flexibility and experimental data. Knegtel RM, Boelens R, Kaptein R Protein Eng. 1994 Jun;7(6):761-7. (4) A method for biomolecular structural recognition and docking allowing conformational flexibility. Sandak B, Nussinov R, Wolfson HJ J Comput Biol. 1998 Winter;5(4):631-54. ----- From: Armin M. Sobhani Just in case you want to know type of interactions, there is a good book that might be interesting: David M. J. Lilley (Ed.), (1995) DNA-Protein: Structural Interactions, IRL Press. ----- From chemistry-request@server.ccl.net Thu Feb 8 07:39:41 2001 Received: from mel.ruc.dk (mel.ruc.dk [130.225.220.27]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f18Cdew08608 for ; Thu, 8 Feb 2001 07:39:40 -0500 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id NAA22480 for ; Thu, 8 Feb 2001 13:39:39 +0100 (MET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id NAA24399 for ; Thu, 8 Feb 2001 13:24:28 +0100 (MET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.44); 8 Feb 01 13:39:40 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.44); 8 Feb 01 13:39:35 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: CHEMISTRY@ccl.net Date: Thu, 8 Feb 2001 13:39:34 +0100 Subject: CCL:DFT for hydrogen bond Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <732E1194F07@virgil.ruc.dk> Dear Yubo Fan: > I know most of DFT methods are not good to the calculation of Hydrogen > Bonding. But a friend of mine told me somebody developed a DFT method > that can be used in HB calculations. What is this method? > > Are there some papers using different methods (DFT methods preferred) to > calculate HB and systematically compare them? Any advice is helpful. The following paper might be of interest to you: J. Spanget-Larsen: "Infrared absorption and Raman scattering of (Z)-3-hydroxypropenal. A density functional theoretical study", Chemical Physics 240 (1999) 51-61. A number of standard DFT procedures (BLYP, BPW91, B3LYP, B3PW91) are applied in a study of molecular and vibrational structure of 3-hydroxypropenal (malonaldehyd enol), probably the simplest species with an intramolecular O..H-O hydrogen-bond. Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~jsl/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Feb 8 11:51:33 2001 Received: from mail-f.bcc.ac.uk (mail-f.bcc.ac.uk [128.40.23.81]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f18GpXw10410 for ; Thu, 8 Feb 2001 11:51:33 -0500 Received: from pat.biochem.ucl.ac.uk by mail-f.bcc.ac.uk with SMTP (Mailer) with ESMTP; Thu, 8 Feb 2001 16:51:21 +0000 Received: from bsmir18 (bsmir18 [128.40.46.21]) by pat.biochem.ucl.ac.uk (8.9.3/8.9.3) with SMTP id QAA07192 for ; Thu, 8 Feb 2001 16:49:13 GMT Date: Thu, 8 Feb 2001 16:49:12 +0000 ("GMT) From: Irilenia Nobeli X-Sender: nobeli@bsmir18 To: Computational Chemistry List Subject: AMP and GMP concentrations: summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Many thanks to James Smith and Doug Markham for their answers to my question regarding relative concentrations of AMP and GMP in a cell. I include the original answers, in case anyone is interested. Irilenia >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > From James.Smith@ddg.phar.cam.ac.uk Fri Feb 2 09:53:36 2001 Purine nucleotides vary in their concentration, due to the localised release and turnover. Local high concentrations may also depend on local divalent cation concentrations (that chelate phosphate groups). Remember eurkaryotic cells are compartmentalised and their organisation is dependent on their specialisation but even oocytes (often used as expression systems) don't have homogenous cytoplasms. If you receive concentration values for intracellular/extracellular purine monophosphate, purine cyclic-monophosphate, purine di and tri phosphate purines be very cautious of the cell type, the method and conditions used. If you have values from different sources in different cell types, the relative values may be more important than the absolute values. Yours sincerely James Smith >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > From gd_markham@fccc.edu Thu Feb 1 21:07:57 2001 There is a long list of nucleotide concentrations in Salmonella in : B.R. Bochner and B.N. Ames, J. Biol. Chem. Vol. 257, p. 9759-9769 (1982) Hope this helps, Doug Markham From chemistry-request@server.ccl.net Thu Feb 8 11:55:40 2001 Received: from mserve1.acs.ucalgary.ca (postfix@mserve1.acs.ucalgary.ca [136.159.34.51]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f18Gtew10461 for ; Thu, 8 Feb 2001 11:55:40 -0500 Received: from ucalgary.ca (acs1.acs.ucalgary.ca [136.159.34.221]) by mserve1.acs.ucalgary.ca (Postfix) with ESMTP id 3FD521126 for ; Thu, 8 Feb 2001 09:55:39 -0700 (MST) Received: from localhost (patchkov@localhost) by ucalgary.ca (AIX4.3/8.9.3/8.8.8) with ESMTP id JAA23106 for ; Thu, 8 Feb 2001 09:55:38 -0700 Date: Thu, 8 Feb 2001 09:55:33 -0700 (MST) From: Serguei Patchkovskii X-Sender: patchkov@acs1.acs.ucalgary.ca To: chemistry@ccl.net Subject: Re: CCL:Linux 2.4.0 and 2 GB promlem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hannes Loeffler wrote: > Yes, it works on Linux/Alpha but not Linux/i386. I am sorry, but that's still false. As others have mentioned, x86 2.4 Linux kernels support files larger than 2Gbytes on ext2 file systems. Although the large file support didn't make it into the previous stable Linux kernel stream, the necessary patches against 2.2 kernels are readily available. In fact, these patches are already included in 2.2 kernels, coming with some pre-packeged distributitions - such as Suse. (Scyld Beowulf distribution also supports large files on x86 - but I do not know whether they use 2.2 kernels) Other Linux distributions, such as Red Hat, have chosen not to include LFS patches into their 2.2 kernels. At the same time, Red Hat 7/x86 ships with LFS-aware libc - so that switching to a 2.4 kernel, or including LFS patches into an RH 2.2 kernel, will give you large file support. Caveat: None of my Linux/x86 systems are used for productuion calculations. As such, I have no direct experience with using LFS-aware x86 Linux kernels. /Serge.P --- Home page: http://www.cobalt.chem.ucalgary.ca/ps/ From chemistry-request@server.ccl.net Thu Feb 8 10:59:38 2001 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f18Fxcw10074 for ; Thu, 8 Feb 2001 10:59:38 -0500 Received: from mail.chem.tamu.edu ([165.91.177.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Thu, 8 Feb 2001 10:11:02 -0600 Sender: yubo@ccl.net Message-ID: <3A826E4D.3EC87803@mail.chem.tamu.edu> Date: Thu, 08 Feb 2001 10:00:45 +0000 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Summary:DFT for hydrogen bond Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit I sent a message about hydrogen bond calculation by DFT to CCL several days ago. I've got many helpful replies. Now I summarize them below. Hi, everyone, I know most of DFT methods are not good to the calculation of Hydrogen Bonding. But a friend of mine told me somebody developed a DFT method that can be used in HB calculations. What is this method? Are there some papers using different methods (DFT methods preferred) to calculate HB and systematically compare them? Any advice is helpful. Thanks in Advance Yubo Fan -- ============================================================ Dr. Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ Hello. I had a couple of such publications a few years back. They are as follows: A. T. Pudzianowski, "A Systematic Appraisal of Density Functional Methodologies for Hydrogen Bonding in Binary Ionic Complexes," J. Phys. Chem. 100(12), 4781-4789 (1996) A. T. Pudzianowski, "Current Computational Approaches to The Strong Hydrogen Bond," Rec. Res. Devel. in Physical Chem. 1, 81-97 (1997). Both of these deal with the strong H-bond, but there are plenty of references to other situations. The latter reference is a review article, so there is lots of related information. It appears in a volume published in India, so it may be hard to find. Let me know if you'd like reprints and I'll send them along. Regards, Andrew Pudzianowski ---------------------------------------- Andrew T. Pudzianowski, Ph.D. Computer-Assisted Drug Design Bristol-Myers Squibb PRI Box 4000 Princeton NJ 08543-4000 (609) 252-4248 (office) (609) 252-6030 (fax) ----------------------------------------- hi Yubo, check B(M)LYP functional which was developed for such calculations (references in the paper enclosed). It's essentially B3LYP whith HF exchange increased to 35%. I've tested it on OH- hydration and it performed quite well. Cheers, Piotr -- Prof. Piotr Paneth temporary address through 5/3/01: Department of Chemistry, Smith Hall box I11, room 224 University of Minnesota Minneapolis, MN 55455-0431 207 Pleasant St. SE phone: (612) 626-0259, fax: (612) 624-9320 or (612) 626-9390 E-mail: paneth@comp.chem.umn.edu or panet001@umn.edu Hi Re: your question to CCL concerning h-bonding and dft. We have been working on a number of H-bonded clusters involving water and have found that the (generally popular) B3LYP method and others give too high "binding". It is suggested that the HTCH functional could be good - this is probably the one you are thinking of. A ref you might find useful is: Tuma, Christian; Daniel Boese, A.; Handy, Nicholas C.. Predicting the binding energies of H-bonded complexes: A comparative DFT study. Phys. Chem. Chem. Phys. (1999), 1(17), 3939-3947. CODEN: PPCPFQ ISSN:1463-9076. CAN 131:342144 AN 1999:538455 CAPLUS and other papers by Handy describing the development of new exchange-correlation functionals. I would be grateful if you summarize or email me any interesting information you get. Cheers, Tim ------------------------------- Tim Robinson Vikings Group Department of Chemistry University of Otago tel 64 3 479 7929 fax 64 3 479 7906 timr@alkali.otago.ac.nz Yubo, actually some of the hybrid DFT does pretty well for H-bonds. Something like B3LYP/6-31+G* gets the water dimer interaction right to about 0.5 kcal/mol. Frank -------------------------------------------------- | Frank Jensen, Department of Chemistry | | SDU Odense University, DK-5230 Odense, Denmark | | FAX +45 66 15 87 80 , Voice +45 65 50 25 07 | | http://www.sdu.dk/Nat/Chem/STAFF/sci/FrjE.html | | http://bogense.chem.ou.dk/~frj | -------------------------------------------------- Try the functionals by Nic Handy (there is one in Gaussian) and also the ones by Baerends. see www.gaussian.com, DFT methods for details or better consult the outstanding book by Koch, Holthausen, VCH 2000 bye Hi Yubo, take a look at the following papers: - Kumar et al., Low barrier hydrogen bonds: Ab initio and DFT Investigations, J. Comp. Chem. 1998, 19, 1345-1352. - C. Tuma et al., Predicting the binding energies of H-Bonded complexes: A comparative DFT study, Phys. Chem. Chem. Phys. (PCCP) 1999, 1, 3939- 3947. -Novoa & Soso, Evaluation of the Density Functional Approximation on the Computation of H-Bond Interactions, J. Phys. Chem. 1995, 99, 15837-15845. - Molecular Dynamics and DFT Studies of Intermolecular Hydrogen Bonds between Bifunctional Heteroazaaromatic Molecules and Hydroxylic Solvents, J.P.C. A; 2000; 104(42); 9542-9555. - Comparative Study of BSSE Correction Methods at DFT and MP2 Levels of Theory (of Hydrogen-bonded clusters), J.Comp.Chem. 1998, 69, 575-584 (and references therein). - Density Functional Theory and Molecular Clusters, J. Comp. Chem. 1995, 16, 1315-1325. - A Systematic Appraisal of Density Functional Methodologies for Hydrogen Bonding in Binary Ionic Complexes," J. Phys. Chem. 100, 4781-4789 (1996). Hopefully you will find something useful. All the best Marc Walter Dear Yubo, I'd say it depends a bit on the system. If the nature of the hydrogen bond is mainly electrostatic, then gradient-corrected and hybrid functional do a reasonably good job. If the nature of the hydrogen bond is mainly dispersive, then DFT won't work. Best regards Klaus -- Dr. Klaus Stark Application Scientist Molecular Simulations Inc. Inselkammerstr. 1 82 008 Unterhaching Germany Phone : ++49-89-61459-420 Mobile : ++49-172-936-3380 Fax : ++49-89-61459-400 E-Mail : kstark@msi.de Web Page : http://www.msi.com Dear Yubo, actually, DFT methods are not really bad for hydrogen bonding, they are just really bad in treating dispersion. They overestimate the electrostatic attraction in order to compensate for the lack of proper treatment of electron correlation. For H-bonded systems, using the B3LYP density functional and the 6-31G(d,p) basis set, you can obtain with quite reasonable geometries and interaction energies. Usually H-bonds are about 0.03A shorter than the they would be when you optimise them with MP2 method and interaction energies are about 5% larger. Density functional calculations on H-bonded systems have been carried out in: M. Meyer, T. Steinke, M. Brandl, J. Sühnel J. Comp. Chem. 2001, 22, 109-124 Density Functional Study of Guanine and Uracil Quartets and of Guanine/Metal Ion Complexes Best regards, Maria Dear Yubo Fan: The following paper might be of interest to you: J. Spanget-Larsen: "Infrared absorption and Raman scattering of (Z)-3-hydroxypropenal. A density functional theoretical study", Chemical Physics 240 (1999) 51-61. A number of standard DFT procedures (BLYP, BPW91, B3LYP, B3PW91) are applied in a study of molecular and vibrational structure of 3-hydroxypropenal (malonaldehyd enol), probably the simplest species with an intramolecular O..H-O hydrogen-bond. Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~jsl/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Thu Feb 8 10:45:07 2001 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f18Fj7w09959 for ; Thu, 8 Feb 2001 10:45:07 -0500 Received: from mail.chem.tamu.edu ([165.91.177.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Thu, 8 Feb 2001 09:56:29 -0600 Sender: yubo@ccl.net Message-ID: <3A826AE4.9ED9845F@mail.chem.tamu.edu> Date: Thu, 08 Feb 2001 09:46:13 +0000 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Summary: CCL:ONIOM and gen cannot work together Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thanks for all replies. I have solve this problem by Ata's advice. Just add two blank lines at the end of the molecular specification input. Below is the question and the replies: Hi, everyone, Today, I tried ONIOM method to calculate a rather big system containing a Nickel atom. I used a modified lanl2dz basis set to Ni and 6-31++G** to all atoms in the directly coordinated groups. B3LYP was used for this part of the molecule. PM3 was used to those substituents on the ligands. The input file is listed below: #P ONIOM(B3LYP/gen:PM3) Pseudo=cards opt scf=(maxcycle=256) freq molecule specification Ni 0 S 3 1.00 0.7620000000D+01 -0.4082550000D+00 0.2294000000D+01 0.7455308000D+00 0.8760000000D+00 0.5325721000D+00 S 4 1.00 0.7620000000D+01 0.1872591000D+00 0.2294000000D+01 -0.3966964000D+00 0.8760000000D+00 -0.4954003000D+00 0.1153000000D+00 0.1084434000D+01 S 1 1.00 0.3960000000D-01 0.1000000000D+01 P 3 1.00 0.2366000000D+02 -0.4815580000D-01 0.2893000000D+01 0.6258473000D+00 0.9435000000D+00 0.4715158000D+00 P 4 1.00 0.2366000000D+02 0.7131470000D-02 0.2893000000D+01 -0.1089909500D+00 0.9435000000D+00 -0.4615260000D-01 0.8400000000D-01 0.8025519700D+00 P 1 1.00 0.2400000000D-01 0.1000000000D+01 D 4 1.00 0.4272000000D+02 0.3726990000D-01 0.1176000000D+02 0.1956103000D+00 0.3817000000D+01 0.4561273000D+00 0.1169000000D+01 0.5621587000D+00 D 1 1.00 0.2836000000D+00 0.1000000000D+01 **** 2 3 4 5 6 7 8 9 10 6-31++G** **** Ni 0 lanl2dz But, this job could not work properly and the following error message was printed in the output file. Standard basis: VSTO-3G (5D, 7F) =============================================================================== ==================================================== PSEUDOPOTENTIAL PARAMETERS =============================================================================== ==================================================== CENTER ATOMIC VALENCE ANGULAR POWER COORDINATES NUMBER NUMBER ELECTRONS MOMENTUM OF R EXPONENT COE FFICIENT X Y Z =============================================================================== ==================================================== WANTED AN INTEGER AS INPUT. FOUND AN END-OF-LINE FOR INPUT. STO-3G ? Error termination via Lnk1e in /usr/local/g98.a7//g98/l301.exe. Cannot G98 work properly when ONIOM and gen are used together? Any advices are prefered. Thanks in advance Yubo -- ============================================================ Dr. Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ ?????????? It's possible, look this example: $RUNGAUSS %chk=teste_mcg.chk #P opt freq oniom(hf/gen:hf/gen) 6d 10f pseudo=cards Gaussian Test: 0 1 0 1 C 0.000000 0.000000 0.000000 H 0.000000 0.000000 1.100000 O 1.125833 0.000000 -0.650000 C -1.299038 0.000000 -0.750000 L H F -1.041506 0.000000 -2.126109 L F -2.033682 -1.142892 -0.412219 L F -2.033682 1.142892 -0.412219 L @./h-0.gbs **** @./c-0.gbs **** @./o-0.gbs **** @./f-0.gbs **** C 0 C 1 2 L=1 COMPONENT 1 1 8.56468 -.89371 L=0 COMPONENT 2 0 2.81497 1.92926 2 8.11296 14.88199 O 0 O 1 2 L=1 COMPONENT 1 1 16.11718 -.92550 L=0 COMPONENT 2 0 5.05348 1.96069 2 15.95333 29.13442 F 0 F 1 2 L=1 COMPONENT 1 1 20.73959 -.93258 L=0 COMPONENT 2 0 6.60488 2.03649 2 18.24092 27.86279 @./h-0.gbs **** @./c-0.gbs **** @./o-0.gbs **** @./f-0.gbs **** C 0 C 1 2 L=1 COMPONENT 1 1 8.56468 -.89371 L=0 COMPONENT 2 0 2.81497 1.92926 2 8.11296 14.88199 O 0 O 1 2 L=1 COMPONENT 1 1 16.11718 -.92550 L=0 COMPONENT 2 0 5.05348 1.96069 2 15.95333 29.13442 F 0 F 1 2 L=1 COMPONENT 1 1 20.73959 -.93258 L=0 COMPONENT 2 0 6.60488 2.03649 2 18.24092 27.86279 In your case it's because PM3 tries read pseudo potentials every time it is executed, so you must "remember" PM3 that there isn't pseudo potentials. Leave more than 2 blank lines at the end of the input and try again (I guess). Ata. -- Ataualpa Albert Carmo Braga atabraga@iqm.unicamp.br http://www.iqm.unicamp.br ????????? Yubo, In my experience, ONIOM has trouble reading pseudopotentials. Although there might be other ways to do it (and I'd love to hear if anyone suggests them), you need to use an IOp to get it to work. With only one QM layer, you might be able to just add IOP(3/17=8) to your route card. Otherwise, you'd need to do a non-standard route, where you include the 17=8 option in any line that begins with 3/5=7... . --Steve Steven Feldgus From chemistry-request@server.ccl.net Thu Feb 8 15:21:00 2001 Received: from yellow.rahul.net (postfix@yellow.rahul.net [192.160.13.18]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f18KKww12413 for ; Thu, 8 Feb 2001 15:20:58 -0500 Received: from foxtrot.rahul.net (foxtrot [192.160.13.6]) by yellow.rahul.net (Postfix) with ESMTP id 0AF2F7C36 for ; Thu, 8 Feb 2001 12:20:59 -0800 (PST) Received: by foxtrot.rahul.net (Postfix, from userid 1448) id C89671DBC; Thu, 8 Feb 2001 12:20:57 -0800 (PST) To: chemistry@ccl.net Subject: Re: CCL:GPL'd MD packages (license for B) References: Message-Id: <20010208202057.C89671DBC@foxtrot.rahul.net> Date: Thu, 8 Feb 2001 12:20:57 -0800 (PST) From: pcm@rahul.net (Peter C. McCluskey) avijit@CS.Cornell.EDU (Avijit Ghosh) writes: > B :: Java based MD Code (couldn't find license on home page) > > http://www.scripps.edu/~nwhite/Biomer/index.html The license is in the source code. It is less restrictive than GPL. -- ------------------------------------------------------------------------------ Peter McCluskey | Fed up with democracy's problems? Examine Futarchy: http://www.rahul.net/pcm | http://hanson.gmu.edu/futarchy.pdf or .ps From chemistry-request@server.ccl.net Thu Feb 8 15:26:52 2001 Received: from ice.lanl.gov (ice.lanl.gov [128.165.22.6]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f18KQmw12478 for ; Thu, 8 Feb 2001 15:26:48 -0500 Received: from localhost (localhost [[UNIX: localhost]]) by ice.lanl.gov (8.9.3/8.9.3) id NAA11568 for CHEMISTRY@ccl.net; Thu, 8 Feb 2001 13:26:43 -0700 From: Matt Challacombe Reply-To: MChalla@LANL.Gov Organization: Group T-12, Theoretical Chemistry and Molecular Physics To: CHEMISTRY@ccl.net Subject: Spring ACS Date: Thu, 8 Feb 2001 13:14:45 -0700 X-Mailer: KMail [version 1.0.29] Content-Type: text/plain References: <732E1194F07@virgil.ruc.dk> In-Reply-To: <732E1194F07@virgil.ruc.dk> MIME-Version: 1.0 Message-Id: <01020813264308.08663@ice> Content-Transfer-Encoding: 8bit Dear Netters, Abstracts for the Spring ACS COMP/PHYS Section on "Methods for Addressing Time and Length Scale Problems in Molecular Simulation" are now available > from my page at http://www.t12.lanl.gov/~mchalla/ This section will cover a range of leading edge research into multi-scale methods for tackling large problems in molecular simulation. Emphasis is in the following subject areas: o Linear Scaling Electronic Structure Theory: density matrix methods, O(N) Fock builds, wavelets o Multiscale Methods: linking atomistic simulation with continuum modeling, QM/MM o Multiple Time Scale Methods: multiple time step methods, advanced sampling methods, accelerated dynamics Sincerely, Matt +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ + Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ + + Los Alamos National Laboratory email: MChalla@LANL.Gov + + Group T-12, Mail Stop B268 phone: (505) 665-5905 + + Los Alamos, New Mexico 87545 fax: (505) 665-3909 + + + + "The secret to mountain biking is pretty simple. The slower you go + + the more likely it is you'll crash." -- Julie Furtado + +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@server.ccl.net Thu Feb 8 15:36:05 2001 Received: from interlock.herc.com (interlock.herc.com [199.221.7.2]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f18Ka5w12579 for ; Thu, 8 Feb 2001 15:36:05 -0500 Received: from csdnsg1.herc.com ([147.116.14.51]) by interlock.herc.com with SMTP id PAA13001 (InterLock SMTP Gateway for ); Thu, 8 Feb 2001 15:36:05 -0500 Subject: crystal structure To: CHEMISTRY@ccl.net Cc: X-Mailer: Lotus Notes Release 5.0.2b December 16, 1999 Message-Id: From: Goutam.Das@betzdearborn.com Date: Thu, 8 Feb 2001 14:34:26 -0600 X-Priority: 3 (Normal) X-Mimetrack: Serialize by Router on CSDNSG1/Servers/Herc(Release 5.0.1b|September 30, 1999) at 02/08/2001 03:23:11 PM Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL'ers I am looking for references/web pages/pointers to the crystal structure of poly alkyl (preferable C16-C24) acrylates which would have the coordinates in a suitable electronic format. I am also interested in the crystal structures of p-alkyl phenol formaldehyde polymers, poly vinyl alcohols, etc Any help will be deeply appreciated. Regards Goutam Das Scientist BetzDearborn Division of Hercules The Woodlands, TX 77380 281.367.6201 ext 425 From chemistry-request@server.ccl.net Thu Feb 8 23:10:40 2001 Received: from mailgw.barc.ernet.in ([202.54.18.131]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f194Acw16521 for ; Thu, 8 Feb 2001 23:10:38 -0500 Received: from apsara.barc.ernet.in (apsara.barc.ernet.in [192.168.1.21]) by mailgw.barc.ernet.in (8.9.3/8.9.3) with ESMTP id JAA44722 for ; Fri, 9 Feb 2001 09:48:33 +0530 (IST) (envelope-from tapang@apsara.barc.ernet.in) Received: from localhost (tapang@localhost) by apsara.barc.ernet.in (8.9.3/8.9.3) with ESMTP id JAA32373 for ; Fri, 9 Feb 2001 09:46:27 +0530 Date: Fri, 9 Feb 2001 09:46:27 +0530 (IST) From: "Dr.Tapan K.Ghanty" To: chemistry@ccl.net Subject: Bilirubin structure Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All, I am looking for the molecular structure of Bilirubin. Calculated structure or X-ray determined structure or any other approximate structure will do my job. Any help will be highly appreciated. With thanks in advance, Dr. Tapan K. Ghanty Theoretical Chemistry Section Chemistry Division Bhabha Atomic Research Centre Trombay, Mumbai 400 085 India From chemistry-request@server.ccl.net Thu Feb 8 16:22:39 2001 Received: from web6203.mail.yahoo.com (web6203.mail.yahoo.com [128.11.22.114]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f18LMcw13389 for ; Thu, 8 Feb 2001 16:22:38 -0500 Message-ID: <20010208212235.27771.qmail@web6203.mail.yahoo.com> Received: from [207.110.20.63] by web6203.mail.yahoo.com; Thu, 08 Feb 2001 13:22:35 PST Date: Thu, 8 Feb 2001 13:22:35 -0800 (PST) From: Iraj Daizadeh Subject: prions To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCL. I was wondering what computational work has been performed in prions. A project on this is of most relevance due to the mad cow follies... Any thoughts? Thanks, Iraj. __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail - only $35 a year! http://personal.mail.yahoo.com/