From adam@cherwell.com Fri Mar 6 06:16:05 1998 Received: from congo.cherwell.com for adam@cherwell.com by www.ccl.net (8.8.3/950822.1) id GAA24246; Fri, 6 Mar 1998 06:01:50 -0500 (EST) Received: from wharfe.cherwell.com ([193.82.249.214]) by congo.cherwell.com (Post.Office MTA v3.1.2 release (PO205-101c) ID# 0-0U10L2S100) with SMTP id AAA274; Fri, 6 Mar 1998 11:01:35 +0000 Message-Id: <1.5.4.32.19980306110128.006f5938@cherwell.com> X-Sender: adam@cherwell.com X-Mailer: Windows Eudora Light Version 1.5.4 (32) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 06 Mar 1998 11:01:28 +0000 To: chemistry@www.ccl.net From: Adam Hodgkin Subject: ChemSymphony Beans: JavaBeans for Chemistry Dear Chemist Cherwell Scientific today announces the release of ChemSymphony Beans. ChemSymphony Beans are customizable and flexible Java tools for creating chemistry resources on a network. The package comprises 36 components or JavaBeans. See: http://www.cherwell.com/chemsymphony/index.html ChemSymphony Beans provide many of the distinctively 'chemical' tools needed for building corporate intranets managing chemistry data; and for integrating the results from (or inputs to) molecular modelling or combinatorial chemistry software over a network. The Beans are components which allow data to be edited and viewed, presented and interactively modified in many different ways. They are standard JavaBeans and can be compiled with other Beans. A variety of 2D and 3D tools are available, and the customizability of JavaBeans will encourage developers and third parties to adapt these basic tools to special purposes. Extensive and detailed documentation which moves from an 'introductory' to an 'advanced programmer' level is available at: http://www.cherwell.com/chemsymphony/ChemSymphonyBeans/index.html We have also posted a White Paper, outlining applications for this technology at: http://www.cherwell.com/chemsymphony/ChemSymphonyBeans/CSBeansUse/CSBeansInt ro.html A fully functional, single-user set of the Beans is available for US$199. Cherwell Scientific also offers annual intranet licences for corporate deployment. Our thanks to the members of the Computational Chemistry List who have helped us at various stages, by providing beta-test reports and suggesting new functionality. Adam --- --- Adam Hodgkin | e-mail: adam@cherwell.com Chairman | Phone: +44 (0)1865 784810 Cherwell Scientific Publishing | Fax: +44 (0)1865 784801 Oxford OX4 4GA, UK | URL: http://www.cherwell.com --- --- From Steven.Creve@chem.kuleuven.ac.be Fri Mar 13 04:17:34 1998 Received: from hartree.quantchem.kuleuven.ac.be for Steven.Creve@chem.kuleuven.ac.be by www.ccl.net (8.8.3/950822.1) id DAA28185; Fri, 13 Mar 1998 03:52:40 -0500 (EST) Received: from localhost (steven@localhost) by hartree.quantchem.kuleuven.ac.be (8.8.7/8.8.7) with SMTP id JAA35136 for ; Fri, 13 Mar 1998 09:54:26 +0100 Date: Fri, 13 Mar 1998 09:54:26 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:G:File sizes Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, does anybody knows if G94 by default limits its scratch file sizes to less than 2 GB ? steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From takanori.kanazawa@pharma.novartis.com Fri Mar 13 06:17:34 1998 Received: from gatekeeper.chbs.ciba.com for takanori.kanazawa@pharma.novartis.com by www.ccl.net (8.8.3/950822.1) id FAA29035; Fri, 13 Mar 1998 05:59:40 -0500 (EST) From: Received: from mailhub by gatekeeper.chbs.ciba.com; (5.65v3.2/1.1.8.2/12Mar96-0208PM) id AA05620; Fri, 13 Mar 1998 11:59:09 +0100 Received: from nts1.novartis.com ([192.168.50.131]) by mta3.is.chbs (8.8.5/8.8.5) with SMTP id LAA07653 for ; Fri, 13 Mar 1998 11:59:33 +0100 (MET) Received: by nts1.novartis.com(Lotus SMTP MTA SMTP MTA v1.1.04 (495.1 10-24-1997)) id 412565C6.003C573F ; Fri, 13 Mar 1998 11:59:04 +0100 X-Lotus-Fromdomain: PH@N1 To: chemistry@www.ccl.net Message-Id: <492565C6.003A3A0F.00@nts1.novartis.com> Date: Fri, 13 Mar 1998 19:58:41 +0900 Subject: G94 geometry optimization with constraints Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers, This is the second time I post here a question. Last time I posted here a question about G94 check point file, I got a lot of answers and I'm grateful to all who gave me replies. This time I have a question about geometry optimization of a dimeric molecule. Each monomer unit is an almost planar molecule except one methyl group. I did geometry optimization of the dimer by fixing the dimer molecule on a plane (dihedral angles between the monomer units is fixed to 0 or 180). In the course of the geometry optimization, intermolecular geometry begins to deviate from planarity and finally the optimization job stops with the following error messages --------------------------------------------------------------------------- ------- Convergence failuer -- run terminated. Error termination via Link1e in /home/Gaussian/g94/l502.exe. Job cpu time: .... ............ --------------------------------------------------------------------------- ------- Before this termination, messages like the following are repeated ------------------------------------------------------------------ Energy Rises -- skip Quadratic search. Quartic linear search produced a step of -0.99578. ....... ....... Iteration 10 RMS(Cart)=************ RMS(Int)=************ Iteration 11 RMS(Cart)=************ RMS(Int)=************ ......... ------------------------------------------------------------------ I guess the reason for this job failuer is that the dihedral angle between monomer units changed abruptly from 0 to 180 or 180 to 0, and the geometry optimization became uncontrollable. Is this right? Is there any way to overcome this problem? I used the default redundant internal coordinate optimization and the keyword "Opt"(not Fopt) I'd appreciate any suggestons very much. With best regards, Takanori ********************************************** Takanori Kanazawa e-mail : takanori.kanazawa@pharma.novartis.com Drug Discovery Group / CAMM Novartis Pharma Japan ********************************************** From Steven.Creve@chem.kuleuven.ac.be Fri Mar 13 11:17:46 1998 Received: from hartree.quantchem.kuleuven.ac.be for Steven.Creve@chem.kuleuven.ac.be by www.ccl.net (8.8.3/950822.1) id KAA00039; Fri, 13 Mar 1998 10:19:14 -0500 (EST) Received: from localhost (steven@localhost) by hartree.quantchem.kuleuven.ac.be (8.8.7/8.8.7) with SMTP id MAA34314 for ; Fri, 13 Mar 1998 12:19:43 +0100 Date: Fri, 13 Mar 1998 12:19:43 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:G: split RWF Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Has anyone succesfully used the %RWF command in G94 in order to split the rwf files over more than one file? (preferrably with AIX) Steven -------------------------------------------------------------------------- Steven Creve steven.creve@chem.kuleuven.ac.be Labo Quantumchemie Celestijnenlaan 200F 3001-HEVERLEE tel: (32) (16) 32 73 93 BELGIUM fax: (32) (16) 32 79 92 From mforster@nibsc.ac.uk Fri Mar 13 11:28:09 1998 Received: from nibsc.ac.uk for mforster@nibsc.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA00081; Fri, 13 Mar 1998 10:24:31 -0500 (EST) Received: from chalsig.nibsc.ac.uk by nibsc.ac.uk via ESMTP (951211.SGI.8.6.12.PATCH1502/940406.SGI.1(NIBSC)) for id LAA07175; Fri, 13 Mar 1998 11:48:43 GMT Received: by chalsig.nibsc.ac.uk (951211.SGI.8.6.12.PATCH1502/client-1.3.1(NIBSC)) id LAA03750; Fri, 13 Mar 1998 11:48:42 GMT Date: Fri, 13 Mar 1998 11:48:42 GMT From: mforster@nibsc.ac.uk (mforster) Message-Id: <199803131148.LAA03750@chalsig.nibsc.ac.uk> To: chemistry@www.ccl.net Subject: intermolecular interactions Dear Net Chemists Could some Quantum chemistry experts please offer some advice or comments on the computation of intermolecular interactions by quantum methods. I noticed a recent paper in which the the difference in the (SCF) energy of an ion pair at some separation (r) relative to the the sum of the energies of the individual ions was used to estimate the stabilisation of the ion pair. Does this approach neglect basis set superposition effects where the 'effective' basis set size grows as the two separate molecules are brought together. In addition how would such calculations be affected by numerical basis sets (eg as used by DMOL). Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel 01707 654753 FAX 01707 646730 E-mail mforster@nibsc.ac.uk