From owner-chemistry@ccl.net Sat Apr 7 10:18:01 2007 From: "irfan ahmad irfandadu-$-yahoo.com" To: CCL Subject: CCL: HOMO and LUMO distribution Message-Id: <-34000-070407064816-6051-KykjFGgRlvxPvBqImnOjaQ-.-server.ccl.net> X-Original-From: irfan ahmad Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 7 Apr 2007 02:48:09 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: irfan ahmad [irfandadu#yahoo.com] I am trying to find the reason of HOMO and LUMO distribution on different ligands.IS it possible to find the reason by using ADF(fragment analysis) or any other test? If someone know,please guide me. ____________________________________________________________________________________ Finding fabulous fares is fun. Let Yahoo! FareChase search your favorite travel sites to find flight and hotel bargains. http://farechase.yahoo.com/promo-generic-14795097 From owner-chemistry@ccl.net Sat Apr 7 10:56:00 2007 From: "Arthit Vongachariya varthit!^!gmail.com" To: CCL Subject: CCL:G: How can run scan relax with lowmethod and singlepoint with highmethod Message-Id: <-34001-070407082219-11003-fV4R8CxEwlVrfle3iJseDw-,-server.ccl.net> X-Original-From: "Arthit Vongachariya" Date: Sat, 7 Apr 2007 08:22:15 -0400 Sent to CCL by: "Arthit Vongachariya" [varthit|,|gmail.com] I used gaussian03 c0.2 for run the job I want to run scan relax for 91 Step with low method(mp2/cc-pvdz) and i want to run singlepoint after relax with high method ( mp4(SDTQ)/cc-pvdz) How can i do ? i test many command for try to run the last,my input is opt(z-matrix,Guided(mp2/cc-pvdz)) mp4 From owner-chemistry@ccl.net Sat Apr 7 11:28:01 2007 From: "Cesar Millan cmp _ buzon.uaem.mx" To: CCL Subject: CCL: Entropy from B-Factors Message-Id: <-34002-070407004915-22386-vVbHBel6tzNtxpHD/CYtqA..server.ccl.net> X-Original-From: "Cesar Millan" Date: Sat, 7 Apr 2007 00:49:12 -0400 Sent to CCL by: "Cesar Millan" [cmp]![buzon.uaem.mx] Hi Everyone, I would like to know if there is any way to estimate the conformational entropy of a protein using the B-factors reported on each crystal structure. Any help would be appreciate. Best Regards. From owner-chemistry@ccl.net Sat Apr 7 13:30:02 2007 From: "Rafi A rafi4dd*gmail.com" To: CCL Subject: CCL: calculation of entropy contribution Message-Id: <-34003-070407130515-26844-blmwIXlZWwMdPzxhHfSJ2w],[server.ccl.net> X-Original-From: "Rafi A" Date: Sat, 7 Apr 2007 13:05:11 -0400 Sent to CCL by: "Rafi A" [rafi4dd:_:gmail.com] Hello everyone, I am trying to calculate the free energy of binding of inhibitors with protein targets. Is there any software or methods that can be used to calculate the entropic contribution to binding free energy of ligand-receptor interactions. I had observed many people use normal mode calculations, but it seems to be very time consuming. Particularly I am interested to know whether I can use molecular dynamics followed by MM-PBSA to calculate MM and solvation energies and use some other software or other empirical methods to calculate entropic contributions. Your suggestions/reply will be very helpful. Regards, Rafi rafi4dd_._gmail.com From owner-chemistry@ccl.net Sat Apr 7 21:41:01 2007 From: "Kalju Kahn kalju%%chem.ucsb.edu" To: CCL Subject: CCL: Method for Frequency Calculations Message-Id: <-34004-070407153145-25016-1nYrv+Wws5NRaONsh6WrNw*server.ccl.net> X-Original-From: Kalju Kahn Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Sat, 07 Apr 2007 12:30:56 -0700 MIME-Version: 1.0 Sent to CCL by: Kalju Kahn [kalju|a|chem.ucsb.edu] Dear Soren, For very small test systems, CCSD(T) and basis set extrapolation give you what most people consider very accurate frequencies. Take a look at a slide set available at http://folk.uio.no/helgaker/talks/ins.pdf Kalju ------------------- > > Sent to CCL by: "Soren Eustis" [soren__jhu.edu] > Disregarding any concerns with processor time and assuming extensive basis > sets, what is generally accepted to be the most accurate method for > frequency calculations of small (non-metallic) molecules? I have heard MP2 > is not that great, but HF and DFT perform better? Am I on the right path > here?> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -+ > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara From owner-chemistry@ccl.net Sat Apr 7 22:16:01 2007 From: "Geoffrey Hutchison geoffh%x%pitt.edu" To: CCL Subject: CCL: ANNOUNCE: Open Babel 2.1 Release Message-Id: <-34005-070407214943-7156-dptICmaajcF4SbQRZJHVMA#server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Date: Sat, 7 Apr 2007 21:49:27 -0400 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Geoffrey Hutchison [geoffh ~ pitt.edu] I am extremely happy to announce the release of Open Babel 2.1.0, the latest stable version of the open source chemistry toolbox. This release represents a major update and should be a stable upgrade, strongly recommended for all users of Open Babel. Highlights include a new framework for molecular mechanics force fields, a framework for canonical, unique atom numbering (i.e., an open source canonical SMILES implementation), new scripting interfaces in Ruby and Java, enhancements to the developer API, several highly-requested file formats, and many, many bug fixes and improvements. What's new? See the full release notes at: http://openbabel.sourceforge.net/wiki/Open_Babel_2.1.0 To download source, see: (Binaries will become available over the next few days) http://sourceforge.net/project/showfiles.php? group_id=40728&package_id=32894&release_id=499413 For more information, see the project website at: http://openbabel.sourceforge.net/ I would like to personally thank a few people for making this release a great one. In alphabetical order, Rich Apodaca, Jean Bréfort, Donald Curtis, Vincent Favre-Nicolin, Benoît Jacob, Craig James and eMolecules.com, Noel O'Boyle, Chris Morley, Tim Vandermeersch, and Fredrik Wallner. This is a community project and we couldn't have made this release without you. Many thanks to all the contributors to Open Babel including those of you who submitted feedback, bug reports, and code. Cheers, -Geoff