From chemistry-request@ccl.net Mon Aug 16 21:07:36 2004 Received: from calmail-be2.berkeley.edu (mailfarm.Berkeley.EDU [128.32.61.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7H27Xfs013101 for ; Mon, 16 Aug 2004 21:07:35 -0500 Received: from [128.32.198.91] (account shaji|at|calmail.berkeley.edu) by calmail-be2.berkeley.edu (CommuniGate Pro WebUser 4.1.8) with HTTP id 1167265; Mon, 16 Aug 2004 19:15:46 -0700 From: "CHEMPATH, SHAJI" Subject: Force constant matrix in G03 output To: chemistry|at|ccl.net Cc: help|at|gaussian.com X-Mailer: CommuniGate Pro WebUser Interface v.4.1.8 Date: Mon, 16 Aug 2004 19:15:46 -0700 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hello CCLers I want to be able to read the cartesian force constant matrix (before diagonalization) from the gaussian output G03 prints out the values for small systems, as below: -------------------------- Copied from G03 output ---------------------------- Force constants in Cartesian coordinates: 1 2 3 4 5 1 0.588973D+00 2 0.351059D-01 0.551344D+00 3 -0.410032D-02 0.423100D-01 0.522460D+00 4 -0.194992D+00 -0.135563D+00 -0.194085D-01 0.201516D+00 5 -0.127794D+00 -0.173118D+00 -0.201655D-01 0.144641D+00 0.196411D+00 -------------------------- Copied from G03 output ---------------------------- For larger molecules it does not print the force matrix. How do I force gaussian to print the force cosntant matrix when I have around 30 atoms in my system? MY TYPICAL INPUT LINE: #p B3LYP/Gen Freq(ReadIso,ReadFC) guess=read geom=check Thanks a lot for your help -------------------------------------------- Shaji Chempath From chemistry-request@ccl.net Tue Aug 17 13:28:31 2004 Received: from calmail-be1.berkeley.edu (mailfarm.Berkeley.EDU [128.32.61.106]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7HISU3d007366 for ; Tue, 17 Aug 2004 13:28:30 -0500 Received: from [128.32.198.91] (account shaji_at_calmail.berkeley.edu) by calmail-be1.berkeley.edu (CommuniGate Pro WebUser 4.1.8) with HTTP id 1182547 for chemistry_at_ccl.net; Tue, 17 Aug 2004 11:36:46 -0700 From: "CHEMPATH, SHAJI" Subject: Fwd: Force constant matrix in G03 output To: chemistry_at_ccl.net X-Mailer: CommuniGate Pro WebUser Interface v.4.1.8 Date: Tue, 17 Aug 2004 11:36:46 -0700 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="_===1182547====calmail-be1.berkeley.edu===_" X-Spam-Status: No, hits=0.3 required=7.5 tests=FCS_URI_NODOTS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part MIME message --_===1182547====calmail-be1.berkeley.edu===_ Content-Type: text/plain; charset="ISO-8859-1"; format="flowed" Content-Transfer-Encoding: 8bit Thanks to Eszter and Tom who pointed out that the values are printed at the end of output file in dense format. Below is the reply from Jim at gaussian who suggested "iop(7/33=1)" as a keyword I have tried this and it works fine Thanks a lot to all of you Shaji -------------------------------------------- Shaji Chempath --- the forwarded message follows --- --_===1182547====calmail-be1.berkeley.edu===_ Content-Type: message/rfc822 Return-Path: Received: from [209.113.151.8] (HELO smtp-test.cshore.com) by calmail-fe2.berkeley.edu (CommuniGate Pro SMTP 4.1.8) with ESMTP id 16591251 for shaji_at_berkeley.edu; Tue, 17 Aug 2004 07:21:47 -0700 Received: from mailsrv.lorentzian.com (unknown [65.113.125.132]) by smtp-test.cshore.com (Postfix) with ESMTP id 78CCAAB32 for ; Tue, 17 Aug 2004 10:21:46 -0400 (EDT) Received: from [193.0.9.112] (unknown [193.0.9.112]) by mailsrv.lorentzian.com (Postfix) with ESMTP id 8BA2FC841 for ; Tue, 17 Aug 2004 10:18:50 -0400 (EDT) Mime-Version: 1.0 (Apple Message framework v609) In-Reply-To: References: Content-Type: text/plain; charset=US-ASCII; format=flowed Message-Id: Content-Transfer-Encoding: 7bit From: Customer Service - Jim Subject: Re: Force constant matrix in G03 output Date: Tue, 17 Aug 2004 10:20:58 -0400 To: "CHEMPATH, SHAJI" X-Mailer: Apple Mail (2.609) Hi Shaji, Gaussian does decrease the amount of printing as the size of the system increases. You can add "iop(7/33=1)" to your list of keywords to get the force constant matrix output, among other matrices, for larger systems. There are several intermediate results included in the output, so make sure you grab the final force constant matrix and not the earlier incomplete values. Regards, Jim Hess On Aug 16, 2004, at 10:15 PM, CHEMPATH, SHAJI wrote: > Hello CCLers > > I want to be able to read the cartesian force constant matrix (before > diagonalization) from the > gaussian output > > G03 prints out the values for small systems, as below: > -------------------------- Copied from G03 output > ---------------------------- > Force constants in Cartesian coordinates: > 1 2 3 4 > 5 > 1 0.588973D+00 > 2 0.351059D-01 0.551344D+00 > 3 -0.410032D-02 0.423100D-01 0.522460D+00 > 4 -0.194992D+00 -0.135563D+00 -0.194085D-01 0.201516D+00 > 5 -0.127794D+00 -0.173118D+00 -0.201655D-01 0.144641D+00 > 0.196411D+00 > -------------------------- Copied from G03 output > ---------------------------- > > For larger molecules it does not print the force matrix. How do I > force gaussian to print the > force cosntant matrix when I have around 30 atoms in my system? > > MY TYPICAL INPUT LINE: > #p B3LYP/Gen Freq(ReadIso,ReadFC) guess=read geom=check > > > > Thanks a lot for your help > > -------------------------------------------- > Shaji Chempath > --_===1182547====calmail-be1.berkeley.edu===_-- From chemistry-request@ccl.net Tue Aug 17 13:30:22 2004 Received: from www.eyesopen.com (eyesopen.com [208.41.78.163]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7HIUK3d007464 for ; Tue, 17 Aug 2004 13:30:20 -0500 Received: from eyesopen.com (208-41-78-162.client.dsl.net [208.41.78.162]) (authenticated) by www.eyesopen.com (8.11.6/8.11.6) with ESMTP id i7HIBF720960 for ; Tue, 17 Aug 2004 12:11:15 -0600 Message-ID: <412250AA.9060805:at:eyesopen.com> Date: Tue, 17 Aug 2004 12:38:34 -0600 From: George Vacek Organization: OpenEye Scientific Software User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.2) Gecko/20030208 Netscape/7.02 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY:at:ccl.net Subject: EON 1.0 - chemical similarity analysis via comparison of electrostatics Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.8 required=7.5 tests=MY_DSL autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net OpenEye Scientific Software, Inc. announces the release of EON 1.0, a program that screens databases of molecules for electrostatic similarity to a lead compound and should contribute significantly to lead generation and library design. Anthony Nicholls, President and Founder of OpenEye, points out "In some of our recent work, which will soon be in press, EON's electrostatics Tanimoto was shown to be an important variable in discriminating classes of active and inactive compounds for the diverse cases of COX2, progesterone, dopamine and the calcium ion channel." EON is an electrostatics comparison program; it compares electrostatic potential maps of aligned molecules and determines a rigorous Tanimoto measure for the comparison, so that the queried molecules can be quickly sorted according to similarity. Such analysis provides an intuitive measure of similarity; the results simply look right. "If you view the electrostatics of two molecules with a high Tanimoto, they clearly look alike, and you expect that they will interact in a similar fashion," says Bob Tolbert, OpenEye's Vice President of Development. "EON is also designed to work with ROCS results, thus yielding compounds with both similar shape and similar electrostatics," emphasizes Tolbert. ROCS rapidly compares 3D molecular shapes, appropriate for screening corporate databases to generate leads with similar shape to known binders of a target protein. Shape and electrostatics are not only whole molecule properties but also fundamental metrics. So they are expected to show significant advantages over 2D descriptors when used for modeling, for example, quantitative structure activity relationships (QSAR). Early users of EON have already remarked on its utility for driving SAR discussions with medicinal chemists, generating electrostatics-based alignments for QSAR models, and hopping to new scaffolds. OpenEye Scientific Software was founded in 1997 to develop large-scale modeling applications and toolkits. Primarily geared towards drug discovery and design, areas of application include structure generation, docking, shape comparison, charge and electrostatics, chemical informatics and visualization. The software is designed for scientific rigor, as well as speed, scalability and platform independence. OpenEye makes most of its technology available as toolkits - programming libraries suitable for custom development. OpenEye software typically is distributable across multiple processors with PVM, supports 64-bit processing, and runs on Linux, Windows and Mac OS X, as well as HP/Compaq, IBM, SGI and SUN flavors of UNIX. For further information, please visit www.eyesopen.com or contact business:at:eyesopen.com. Regards, George Vacek VP, Business Development OpenEye Scientific Software From chemistry-request@ccl.net Tue Aug 17 09:24:01 2004 Received: from sesosn01.astrazeneca.com (sesosn01.astrazeneca.com [212.209.42.131]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i7HEO03d024489 for ; Tue, 17 Aug 2004 09:24:00 -0500 Received: from sesosn11.seso.astrazeneca.net (sesosn11.seso.astrazeneca.net [192.168.199.18]) by sesosn01.astrazeneca.com (8.12.11/8.12.11) with ESMTP id i7HEW8vm006729 for ; Tue, 17 Aug 2004 16:32:15 +0200 (MET DST) Received: from sesosn21.seso.astrazeneca.net (sesosn21.seso.astrazeneca.net [192.71.145.181]) by sesosn11.seso.astrazeneca.net (8.12.11/8.12.11/AZ-def_main_in.12.11.0) with ESMTP id i7HEV43e000540 for ; Tue, 17 Aug 2004 16:31:08 +0200 (MET DST) Received: from astra-cdc-x03.seso.astrazeneca.net (astra-cdc-x03.seso.astrazeneca.net [192.71.145.48]) by sesosn21.seso.astrazeneca.net (8.12.11/8.12.11) with ESMTP id i7HEV3eb007953 for ; Tue, 17 Aug 2004 16:31:04 +0200 (MET DST) Received: by astra-cdc-x03.seso.astrazeneca.net with Internet Mail Service (5.5.2653.19) id ; Tue, 17 Aug 2004 16:29:44 +0200 Message-ID: <7AAAA741F386B04390FCD7FB61F915466C9823$at$usbodmsx01.rd.astrazeneca.net> From: Michelle.Lamb$at$astrazeneca.com To: chemistry$at$ccl.net Subject: ACS COMP Division: Fall 2004 Newsletter Date: Tue, 17 Aug 2004 16:26:22 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net The Fall 2004 ACS COMP Division newsletter is currently available on the web at: http://www.balbes.com/fall04.pdf for those who would like to access it prior to the National Meeting starting this weekend in Philadelphia. In the near future it will be available, along with past newsletters, on the COMP Division website via: http://membership.acs.org/C/COMP/newsletters/index.html Michelle Lamb Newsletter Editor, ACS COMP Division Michelle.Lamb$at$astrazeneca.com