From owner-chemistry@ccl.net Mon Jan 2 12:59:00 2006 From: "Alex Allardyce aa . chemaxon.hu" To: CCL Subject: CCL: ChemAxon: Free provision for non-commercial freely accessible websites Message-Id: <-30414-060102125748-8318-iPxnEyliMUm+MFvZ1yhEEQ : server.ccl.net> X-Original-From: "Alex Allardyce" Sent to CCL by: "Alex Allardyce" [aa-$-chemaxon.hu] please excuse cross postings ChemAxon announces the launch of the "FreeWeb" package to provide it's chemical editing, viewing, search, property calculation and database management toolkits at no cost to freely accessible web resources being operated for non-commercial purposes. In addition to unlimited licenses, upgrades and support will be provided. Following from the success of ChemAxon's Academic Package, which gives all products free for academic teaching and research, the FreeWeb package aims to increase the quality and capabilities of publicly accessible online chemical research resources. Toolkits included within the package: The Marvin Java applet family for creating chemical queries, viewing results and ligand/macromolecular analysis; JChem Base and JChem Cartridge to allow chemical searching and database management; Standardiser allowing business rules for structure management and Calculator Plugins to provide a range of structure based properties interesting to researchers for content held by the provider. For more information please see this link at our website: http://www.chemaxon.com/prices.html To see the press release source at the PRNewswire website, please visit: http://www.prnewswire.com/cgi-bin/stories.pl?ACCT=104&STORY=/www/story/01-02-2006/0004241093&EDATE= From owner-chemistry@ccl.net Mon Jan 2 13:53:00 2006 From: "Satyan Sharma satyan-.-sun3.oulu.fi" To: CCL Subject: CCL:G: ONIOM Convergence Message-Id: <-30415-060102134507-917-O2AbIsL4llDsU18CaH+hRA*server.ccl.net> X-Original-From: Satyan Sharma Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 02 Jan 2006 19:47:30 +0200 MIME-Version: 1.0 Sent to CCL by: Satyan Sharma [satyan(-)sun3.oulu.fi] Dear CCLers, I am trying to do ONIOM (B3LYP/6-31G*:Amber)optimization of an active site to study the reaction. The optimization of reactants with Mechanical Embeding went fine but I am facing problems with Electronic Embedding. One of the imp. residue in QM level is just exploding. De. Douglas Fox asked me to look at the actual forces and charges.I am pasting a part of my lof file. ***** Axes restored to original set ***** Cartesian Forces: Max 0.152472953 RMS 0.017881355 SvSCFP is copying densities from files 528 and 530 to 603. ONIOM: saving gridpoint 2 ONIOM: restoring gridpoint 1 ONIOM: generating point 1 -- low level on model system. ChrgS2: IScale= 0 0 5 5 5 5 Standard basis: EHTBasis (5D, 7F) There are 99 symmetry adapted basis functions of A symmetry. Integral buffers will be 131072 words long. Raffenetti 1 integral format. Two-electron integral symmetry is turned on. 99 basis functions, 297 primitive gaussians, 99 cartesian basis functions 58 alpha electrons 58 beta electrons nuclear repulsion energy 803.9533589166 Hartrees. Warning! P atom 884 may be hypervalent but has no d functions. NAtoms= 892 NActive= 36 NUniq= 36 SFac= 1.00D+00 NAtFMM= 60 Big=F AMBER calculation of energy and first derivatives. MO and density RWFs will be updated without deorthogonalization. Energy= -16.234481764461 NIter= 0. Dipole moment= 35.284478 -23.726393 15.589231 ***** Axes restored to original set ***** Cartesian Forces: Max 0.944035307 RMS 0.046767678 ONIOM: saving gridpoint 1 ONIOM: restoring gridpoint 3 ChrgS2: IScale= 0 0 5 5 5 5 Using ESP charges for embedding optimization. NRF= 0 NRA= 0 NVA= 717 HaveQM=F Convergence limit is 0.300E-04 MaxStp= 3726 StMxLn= 1.00D-04 StpMin= 1.00D-06. Convergence criteria 0.00004500 0.00003000 0.00018000 0.00012000 Step NS ND Rises OKQ Scale Max. Force RMS Force Max. Disp. RMS Disp. Energy Flag 1 0 0 F T 1.00D+00******************************************** 956.0120774 ---- 2 0 0 T F 6.64D-01********************************************************* ---- 3 0 0 T F 3.04D-01********************************************************* ---- 4 0 0 T F 3.24D-01*********************************32.86966644************* ---- 5 0 0 T F 3.30D-01*********************************10.6392549236470.3982773 ---- 6 0 0 T F 3.33D-01********************************* 3.51412482 3939.3238116 ---- 7 0 0 F F -6.66D-01**********************50.78738958 1.16945260 477.9708826 ---- 8 0 0 F F 3.30D-01**********************33.80141423 0.77832612 125.7750919 ---- 9 0 0 F F -3.22D-01**********************11.16786934 0.25715623 110.3916057 ---- 10 0 0 T F 3.84D-01********************** 3.59603897 0.08280396 114.7644448 ---- 11 0 0 F F 4.68D-01********************** 1.38191027 0.03182047 103.5560777 ---- 12 0 0 T F 2.98D-01********************** 0.64626587 0.01488120 103.9430473 ---- 13 0 0 F F -1.29D-01********************** 0.19290065 0.00444181 103.5206525 ---- 14 0 0 F F -1.62D-02********************** 0.02488053 0.00057291 103.5198560 ---- 15 0 0 F T 1.00D+0040.51468106 1.1411003440.52395915 1.14112839 103.5198558 ---- 16 0 0 T F 6.63D-0140.51468106 1.1411003440.52395915 1.14112839************* ---- 17 0 0 T F 5.00D-0140.51468106 1.1411003426.85920897 0.75633789 1903.4419365 ---- 18 0 0 T F 6.19D-0140.51468106 1.1411003413.42960449 0.37816895 999.2906879 ---- 19 0 0 F F -6.23D-0140.51468106 1.14110034 8.31785482 0.23422539 101.6681627 ---- 20 0 0 F F -4.22D-0140.51468106 1.14110034 5.18319138 0.14595531 89.4935129 ---- 21 0 0 F F -2.42D-0140.51468106 1.14110034 2.18928416 0.06164882 83.1083627 ---- Any suggestions. regards, Satyan