From gdurst@dowelanco.com Wed Jul 16 09:07:30 1997 Received: from elinet1.dowelanco.com for gdurst@dowelanco.com by www.ccl.net (8.8.3/950822.1) id JAA07008; Wed, 16 Jul 1997 09:03:28 -0400 (EDT) Received: by elinet1.dowelanco.com id AA20880 (InterLock SMTP Gateway 3.0 for chemistry@www.ccl.net); Wed, 16 Jul 1997 08:03:18 -0500 Received: by elinet1.dowelanco.com (Internal Mail Agent-1); Wed, 16 Jul 1997 08:03:18 -0500 Message-Id: From: "Durst, Gregory L." To: "'chemistry@www.ccl.net'" Subject: re:reaction pathway program Date: Wed, 16 Jul 1997 08:04:29 -0500 X-Mailer: Microsoft Exchange Server Internet Mail Connector Version 4.0.994.63 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit regarding the message... > >Do you know of any (engineering, chemistry, biological, etc) program that >given a compound would suggest any and all reaction pathways toward that >compound (no matter how outlandish from a thermodyanmic standpoint)? > I am aware of the 'Chiron' program that features computer assisted reaction schemes, stereochemical analysis and precursor selection. It has a 3D drawing module and molecule manipulation. The prorgam runs >from databases that were meticulously created for the explicit purpose of reaction planning. Platforms supported are Macintosh and SGI. For more info contact: Prof. S. Hanessian Department of Chemistry Universite of Montreal PO Box 6128, Station A Montreal, Quebec H3C 3J7 Canada email - hanessia@ere.umontreal.ca fax - 514/343-5728 Regards, Greg +---------------------------------------------------------------------+ | Gregory L. Durst Computational Chemistry | | phone: 317/337-3413 DowElanco R&D | | email: gdurst@dowelanco.com 9330 Zionsville Rd. 306/D2 | | Indianapolis, IN 46268 USA | +---------------------------------------------------------------------+ From D.A.Tilbrook@mds.qmw.ac.uk Wed Jul 16 10:07:29 1997 Received: from netsrv.lhmc.ac.uk for D.A.Tilbrook@mds.qmw.ac.uk by www.ccl.net (8.8.3/950822.1) id JAA07114; Wed, 16 Jul 1997 09:20:25 -0400 (EDT) Received: from lhmc-fs.mds.qmw.ac.uk (LHMC-FS.lhmc.ac.uk [161.23.16.195]) by netsrv.lhmc.ac.uk (8.6.12/8.6.12) with ESMTP id OAA08848 for ; Wed, 16 Jul 1997 14:21:30 +0100 Received: from LHMC/SMTPMAIL by lhmc-fs.mds.qmw.ac.uk (Mercury 1.21); 16 Jul 97 14:16:39 GMT0BST Received: from SMTPMAIL by LHMC (Mercury 1.21); 16 Jul 97 14:16:37 GMT0BST From: "David A Tilbrook (DMS) 3241" Organization: St. Bart's and the Royal London Med To: chemistry@www.ccl.net Date: Wed, 16 Jul 1997 14:16:37 GMT0BST Subject: London based AMBER Users......??? X-Confirm-Reading-To: "David A Tilbrook (DMS) 3241" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail v3.22 Message-ID: <100FF5143D38@lhmc-fs.mds.qmw.ac.uk> Dear List, I am working in conjuction with a colleague at the IRC in Biomedical Materials who has an interest in using molecular modelling to study water adsorption by biomaterials and chemical aspects of drug release and targetting. As a low cost option we are looking at starting our studies using the AMBER force field. I would be very grateful to hear from any users in the London area who are using this package and who have experience with the LEAP interface for structure generation. Perhaps we could start a dialogue which might be mutually beneficial. As we are going to start of by running on high-spec pentiums we will need to compile the source code under Linux. If you have experience of this I would be extremely interested to hear from you.... Look forward to your responses....many thanks in advance David Tilbrook D.A.Tilbrook@mds.qmw.ac.uk********************************************************** David A. Tilbrook Biomaterials in Relation to Dentistry IRC in Biomedical Materials, B.M.S 2.21.2 Queen Mary and Westfield College (East Gate), Mile End Road, London E1 4NS Tel: 0171 2957974 Fax: 0171 2957979 e-mail D.A.Tilbrook@mds.qmw.ac.uk ********************************************************** From gbarbeau@eagle.ibc.edu Wed Jul 16 11:07:29 1997 Received: from eagle.ibc.edu for gbarbeau@eagle.ibc.edu by www.ccl.net (8.8.3/950822.1) id KAA07563; Wed, 16 Jul 1997 10:50:32 -0400 (EDT) Received: from localhost by eagle.ibc.edu (5.65/1.35) id AA14864; Wed, 16 Jul 97 10:43:58 -0500 Date: Wed, 16 Jul 1997 10:43:57 -0500 (CDT) From: Gina Barbeau To: chemistry@www.ccl.net Subject: A request for help on molecular modeling simulations. Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am an undergrad Biochem student doing summer research on ligand-receptor interactions. I would like to know what are good energy values to expect when docking the protein ligand to the protein receptor. What kind of values should I be looking for in the VDW, the electrical energy, and the overall energy? How do I estimate that the energy is a good docking of the two? The software that I have to work with is Insight II on the SGI. I would also appreciate any suggestions as to what minimization and dynamics algorithms to use on Discover once I dock the two together to get a better idea of "docked" conformation. In advance, thank you for your help. G. Barbeau email: gbarbeau@eagle.ibc.edu From Steven.Creve@chem.kuleuven.ac.be Wed Jul 16 11:13:43 1997 Received: from hartree.quantchem.kuleuven.ac.be for Steven.Creve@chem.kuleuven.ac.be by www.ccl.net (8.8.3/950822.1) id KAA07373; Wed, 16 Jul 1997 10:15:23 -0400 (EDT) Received: from localhost by hartree.quantchem.kuleuven.ac.be with SMTP id AA36274 (5.67c/IDA-1.5 for ); Wed, 16 Jul 1997 16:15:49 +0100 Date: Wed, 16 Jul 1997 16:15:48 +0100 (NFT) From: Steven Creve To: Computational Chemistry List Subject: CCL:G: BUG in G94 C.3 Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi. There seems to be (another) bug in Gaussian94 rev C.3 The calculation of the total electronic density yielded an asymmetric density for a symmetric molecule. This did not happen when using rev E.2 The asymmetric densities were found for H2CCO- and H2CCO+. not for the neutral species. Has anyone encountere this or a similar bug? Steven. Here is my input file: $RunGauss %chk=rho %mem=3500000 # HF/cc-pVDZ DENSITY=current CUBE=(cards,density,full) H2C=C=O using HF/6-311+G(d,p) geom 0 1 C .000000 .000000 -1.207285 C .000000 .000000 .102676 O .000000 .000000 1.264130 H .000000 .938273 -1.742691 H .000000 -.938273 -1.742691 /home/steven/test/rhoneutryz -1 0.000000 -2.000000 -2.000000 1 0.000000 0.000000 0.000000 100 0.000000 0.040000 0.000000 100 0.000000 0.000000 0.040000 --Link1-- $RunGauss %chk=rho %mem=3500000 # HF/cc-pVDZ DENSITY=current CUBE=(cards,density,full) H2C=C=O using HF/6-311+G(d,p) geom -1 2 C .000000 .000000 -1.207285 C .000000 .000000 .102676 O .000000 .000000 1.264130 H .000000 .938273 -1.742691 H .000000 -.938273 -1.742691 /home/steven/test/rhoanionyz -1 0.000000 -2.000000 -2.000000 1 0.000000 0.000000 0.000000 100 0.000000 0.040000 0.000000 100 0.000000 0.000000 0.040000 --Link1-- $RunGauss %chk=rho %mem=3500000 # HF/cc-pVDZ DENSITY=current CUBE=(cards,density,full) H2C=C=O using HF/6-311+G(d,p) geom +1 2 C .000000 .000000 -1.207285 C .000000 .000000 .102676 O .000000 .000000 1.264130 H .000000 .938273 -1.742691 H .000000 -.938273 -1.742691 /home/steven/test/rhokationyz -1 0.000000 -2.000000 -2.000000 1 0.000000 0.000000 0.000000 100 0.000000 0.040000 0.000000 100 0.000000 0.000000 0.040000 -------------------------------------------------------------------------- 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 elewars@alchemy.chem.utoronto.ca Wed Jul 16 12:07:32 1997 Received: from alchemy.chem.utoronto.ca for elewars@alchemy.chem.utoronto.ca by www.ccl.net (8.8.3/950822.1) id LAA07690; Wed, 16 Jul 1997 11:12:50 -0400 (EDT) Received: (from elewars@localhost) by alchemy.chem.utoronto.ca (8.7.4/8.7.3) id LAA14072 for chemistry@www.ccl.net; Wed, 16 Jul 1997 11:12:40 -0400 (EDT) Date: Wed, 16 Jul 1997 11:12:40 -0400 (EDT) From: "E. Lewars" Message-Id: <199707161512.LAA14072@alchemy.chem.utoronto.ca> To: chemistry@www.ccl.net Subject: PROGRAM FOR SYNTHETIC ROUTES Hello, regarding the question: > 14-JUL-1997 19:23:06.01 >From: IN%"jtgolab@amoco.com" >To: IN%"CHEMISTRY@www.ccl.net" >CC: IN%"jtgolab@amoco.com" >Subj: CCL:Reaction Pathway Program > >Dear CCL Member: > >Do you know of any (engineering, chemistry, biological, etc) program that >given a compound would suggest any and all reaction pathways toward that >compound (no matter how outlandish from a thermodyanmic standpoint)? > >For example, given tolune, the program would suggest: > > 1) benzene + methane -> toluene > 2) methylcyclohexane -> toluene + H2 > 3) methane + heat/pressure -> toluene + H2 > 4) ETC. > >Perhaps this is really a database that is part of a program. Any leads >would be gratefully appreciated! Thanks. > >-- > >:Joe > > jtgolab@amoco.com > (630) 961-7878 > > +-------------------------------------------------------------------------+ > | There are two kinds of people, those who finish what they start and ... | > | - Robert Byrne | > +-------------------------------------------------------------------------+ ---------------- I don't know of of a program that would give all the "paper paths" to a given molecule, but there are organic synthesis programs that will give _reasonable_ routes to a target molecule, some of them routes that a human might well overlook. A simple such program, Syntree, is (was?) available from the ACS for ca. $200; a much more elaborate program, LHASA, is available from Harvard. Work on programs like these was initiated in the 1960's by E. J. Corey (Nobel Prize 1990) and coworkers. E. Lewars ===================== From itsigeln@chem.ucsd.edu Wed Jul 16 13:07:30 1997 Received: from mailbox1.ucsd.edu for itsigeln@chem.ucsd.edu by www.ccl.net (8.8.3/950822.1) id NAA08248; Wed, 16 Jul 1997 13:03:58 -0400 (EDT) Received: from checfs2 (checfs2.ucsd.edu [132.239.73.6]) by mailbox1.ucsd.edu (8.8.5/8.6.9) with SMTP id KAA26486 for ; Wed, 16 Jul 1997 10:03:58 -0700 (PDT) Received: from chemod0-fddi.ucsd.edu by checfs2 (SMI-8.6/UCSDPSEUDO.4) id KAA23944 for ; Wed, 16 Jul 1997 10:03:57 -0700 Received: by chemod0-fddi.ucsd.edu (951211.SGI.8.6.12.PATCH1502) id KAA21122; Wed, 16 Jul 1997 10:08:19 -0700 Date: Wed, 16 Jul 1997 10:08:19 -0700 From: itsigeln@chem.ucsd.edu (Igor Tsigelny) Message-Id: <199707161708.KAA21122@chemod0-fddi.ucsd.edu> To: CHEMISTRY@www.ccl.net Subject: phosphothreonine charges Hi CCL members, I try to find the partial charges for phosphothreonine and phosphoserine for AMBER or CHARMM forcefields. Can you give me some leads. Sincerely Igor From nauss@beryllium.crs.uc.edu Wed Jul 16 16:07:40 1997 Received: from beryllium.crs.uc.edu for nauss@beryllium.crs.uc.edu by www.ccl.net (8.8.3/950822.1) id QAA08908; Wed, 16 Jul 1997 16:06:42 -0400 (EDT) Received: (from nauss@localhost) by beryllium.crs.uc.edu (8.8.5/8.8.5) id QAA15726 for chemistry@www.ccl.net; Wed, 16 Jul 1997 16:06:43 -0400 (EDT) From: nauss@beryllium.crs.uc.edu (Jeffrey L. Nauss) Message-Id: <9707161606.ZM15724@beryllium.crs.uc.edu> Date: Wed, 16 Jul 1997 16:06:42 -0400 Organization: Dept. Chemistry, University of Cincinnati Reply-to: Jeffrey.Nauss@UC.Edu X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net Subject: Compiling AMBER 4.1 on a Power Challenge Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii I am trying to compile AMBER 4.1 on a Power Challenge. The uname -a output is "IRIX64 bebop 6.1 07121823 IP21 mips". Specifically, I am trying to get leap compiled. However the compilation bombs during the command: make World >& mkerr & The error message at the end of the mkerr file is: /usr/bin/cc -o utilMakeHelp -g -DMEMORY_DEBUG=0 -I.. -cckr -noprototypes -w -Wf,-XNl16386 -xansi -32 -Wf,-XNh2000 basics.o sysdepend.o stringExtra.o varArray.o getline.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o utilMakeHelp.o -nostdlib -L/usr/lib -lm ld: FATAL 12: Object class error (/usr/lib/crt1.o): not a 32-bit object. *** Error code 1 (bu21) *** Error code 1 (bu21) *** Error code 1 (bu21) Anybody have a clue what I need to do? I have already tried removing all -32 options from the Makefile and got the same error. Thanks in advance... -- Jeffrey L. Nauss, PhD Telephone: 513-556-0148 Dir. Molec. Model. Serv. Fax: 513-556-9239 Department of Chemistry e-mail: Jeffrey.Nauss@UC.Edu University of Cincinnati URL http://www.che.uc.edu/~nauss