From frj@dou.dk Thu Sep 29 03:11:02 1994 Received: from danpost.uni-c.dk for frj@dou.dk by www.ccl.net (8.6.9/930601.1506) id DAA08048; Thu, 29 Sep 1994 03:00:26 -0400 Received: from localhost (ean@localhost) by danpost.uni-c.dk (8.6.4/8.6) id IAA22028 for chemistry@ccl.net; Thu, 29 Sep 1994 08:00:24 +0100 Date: 29 Sep 94 8:00 +0100 From: Frank Jensen To: chemistry@ccl.net Message-ID: <1253*frj@dou.dk> Subject: Uphill IRC Antonio Ramos asked for a method for following the IRC uphiill >from the minimum to the TS, and Ron Shepard made some comments on this. I have recently done some analysis on current methods for walking uphill along normal modes from a minimum to a TS. The main findings are: 1) It will be virtually impossible to follow the IRC uphill 2) There may exist paths which resemble the IRC, and which lead from the same minimum to the same TS as the IRC, but differ in the exact path. 3) These alternative paths may be followed uphill, but only if they start from the lowest normal mode (of a given symmetry) at the minimum. The common claim in the literature that one can find TS's by walking up "higher" modes appears to be false. 4) Many methods can walk up the lowest mode, including the OPT=EF included in Gaussian. Frank From Thomas.Kowall@icma.unil.ch Thu Sep 29 09:12:23 1994 Received: from uldns1.unil.ch for Thomas.Kowall@icma.unil.ch by www.ccl.net (8.6.9/930601.1506) id JAA15951; Thu, 29 Sep 1994 09:08:54 -0400 Received: from cisun2000.unil.ch (actually cisun2000) by uldns1 with SMTP (PP); Thu, 29 Sep 1994 14:08:51 +0100 Received: by cisun2000.unil.ch (5.x/Unil-3.1/) id AA28297; Thu, 29 Sep 1994 14:08:48 +0100 Date: Thu, 29 Sep 1994 14:08:48 +0100 From: Thomas.Kowall@icma.unil.ch (Thomas KOWALL) Message-Id: <9409291308.AA28297@cisun2000.unil.ch> To: chemistry@ccl.net Subject: N,N-dimethylformamide, computer simulation X-Sun-Charset: US-ASCII Dear CCListers, I am looking for published computer simulation studies and interaction potentials for liquid N,N-dimethylformamide (DMF). Any hints and pointers are highly welcome. Thomas Kowall ---------------------------------------------------------------- Thomas Kowall ICMA Universite de Lausanne Batiment de chimie (BCH) CH-1015 Lausanne e-mail: tkowall@icma.unil.ch From san@mbu.iisc.ernet.in Thu Sep 29 09:20:17 1994 Received: from sangam.ncst.ernet.in for san@mbu.iisc.ernet.in by www.ccl.net (8.6.9/930601.1506) id IAA14804; Thu, 29 Sep 1994 08:11:04 -0400 From: Received: from soochak.ncst.ernet.in (soochak.ncst.ernet.in [144.16.11.100]) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with ESMTP id RAA03205 for ; Thu, 29 Sep 1994 17:40:17 +0500 Received: from nic.iisc.ernet.in (twisha.ece.iisc.ernet.in [144.16.64.4]) by soochak.ncst.ernet.in (8.6.8.1/8.6.5) with SMTP id RAA15304 for ; Thu, 29 Sep 1994 17:39:22 +0530 Received: by nic.iisc.ernet.in (ERNET-IISc/AT&T UNIX SYS V.3.2) id AA12382; Thu, 29 Sep 94 17:38:53 EST Date: Thu, 29 Sep 94 17:38:53 EST Message-Id: <9409292238.AA12382@nic.iisc.ernet.in> Received: by vigyan.iisc.ernet.in (smail2.3) id AA05995; 29 Sep 94 13:34:54 EST (Thu) To: vigyan!chemistry@ccl.net Subject: helical wheel plots Hi Netters, Can anybody tell me the source to a get the program that plots helical wheel diagram given the sequence of an alpha helix. expecting a quick response thank you sandeep kumar san@mbu.iisc.ernet.in i will sumarize to the net if i get enough responses. From Jeffrey.Gosper@brunel.ac.uk Thu Sep 29 10:11:07 1994 Received: from monge.brunel.ac.uk for Jeffrey.Gosper@brunel.ac.uk by www.ccl.net (8.6.9/930601.1506) id JAA17036; Thu, 29 Sep 1994 09:55:30 -0400 Received: from chem-pc-13.brunel.ac.uk by monge.brunel.ac.uk with SMTP (PP) id <00762-0@monge.brunel.ac.uk>; Thu, 29 Sep 1994 14:54:52 +0100 Date: Thu, 29 Sep 1994 14:55:01 BST From: Jeffrey J Gosper Reply-To: Jeffrey.Gosper@brunel.ac.uk Subject: Mopac reaction coord viewer (for windows) To: chemistry@ccl.net Message-ID: Priority: Normal MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear fellow computational chemists, I have recently finished programming a Windows 3.1 application that generates a concatinated XYZ formatted sturcture file for a Mopac (6) output file which has been generated using a reaction path type calculation. The program extracts the coordinate data for all steps (or alternatively a user defined step) and stores this to a file. The program also provides a 3D molecular viewer which enables any of the steps to be displayed and even animation of the reaction pathway. I am trying to gauge the interest others may have in such a program and wish to have some others (alpha) test and comment on it. If your interested in trying this program please contact me. If there is enough interest (and willing 'testers') I'll probably make the program available over the net at some later date. N.B. I also have added a facility for generating POV (raytracing) input files from xyz coordinates. As POV is Freeware and produces high quality 'real looking' images some of the pictures I've are pretty interesting. My program linked to POV does a very similar job to that that jmr_bs does. Again if there is real interest in this sort of program out there let me know. Cheers from Brunel Jeff Gosper From joel@goodson.chem.smu.edu Thu Sep 29 13:11:08 1994 Received: from goodson.chem.smu.edu for joel@goodson.chem.smu.edu by www.ccl.net (8.6.9/930601.1506) id MAA20736; Thu, 29 Sep 1994 12:40:27 -0400 Received: by goodson.chem.smu.edu (/\==/\ Smail3.1.28.1 #28.1) id ; Thu, 29 Sep 94 11:41 CDT Message-Id: From: joel@goodson.chem.smu.edu (Joel Cohen) Subject: freeby fortran To: chemistry@ccl.net Date: Thu, 29 Sep 1994 11:41:54 -0500 (CDT) X-Mailer: ELM [version 2.4 PL21] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 172 Hi netters, I'm looking for a reliable public domain FORTRAN for my pc. Maybe you guys can help. Dr. Joel Cohen Chemical Physics Superhero From hou@agouron.com Thu Sep 29 13:18:45 1994 Received: from agouron.com for hou@agouron.com by www.ccl.net (8.6.9/930601.1506) id MAA20852; Thu, 29 Sep 1994 12:47:57 -0400 Received: from duck.agouron.com by agouron.com via SMTP (940715.SGI.52/930901.SGI) for CHEMISTRY@ccl.net id AA17631; Thu, 29 Sep 94 09:48:23 -0700 Received: by duck (940406.SGI/931108.SGI.ANONFTP) for @tbone.agouron.com:CHEMISTRY@ccl.net id AA18537; Thu, 29 Sep 94 09:52:42 -0700 Date: Thu, 29 Sep 94 09:52:42 -0700 From: hou@agouron.com (Xinjun Hou) Message-Id: <9409291652.AA18537@duck> To: CHEMISTRY@ccl.net Subject: CHARMM charge assignment > The alternatives > usually involve either (1) models such as Mulliken charges > which do not necessarily reproduce the molecular electrostatic > potential or (2) empirically derived charges such as those > fit to reproduce interaction energies and distances (CHARMM) > or liquid properties (OPLS). Because electrostatic potential >.... Is there any reference on charge assignment method for CHARMM, and/or CHARMm? C Xinjun J. Hou hou@agouron.com C Agouron Pharmaceuticals, Inc. #include C10110000110100101101110011010100111010101101110010010000110111101110101 From criscuol@gensia.edu Thu Sep 29 13:19:57 1994 Received: from genny.gensia.com for criscuol@gensia.edu by www.ccl.net (8.6.9/930601.1506) id MAA20397; Thu, 29 Sep 1994 12:16:19 -0400 Received: from localhost.gensia.com by genny.gensia.com via SMTP (931110.SGI/920502.SGI) for CHEMISTRY@ccl.net id AA01764; Thu, 29 Sep 94 06:51:05 -0700 Date: Thu, 29 Sep 1994 06:39:02 -7178624 (PDT) From: Fred Criscuolo Sender: criscuol@gensia.edu Reply-To: criscuol@gensia.edu Subject: Gaussian92 run time problem under AIX 3.2.5 To: CHEMISTRY@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII We are running Gaissian92 on a RS/6000 Model 590 under AIX 3.2.5. One of the users here is unable to complete his runs because his integral storage file is attempting to exceed the 2GB file size limit imposed by AIX 3.2. According to this user, his model consists of 250 basis functions and he is already using direct SCF. I have investigated upgarding our systems to AIX 4.1 to get around this limitation. Unfortunately, while AIX 4.1 allows filesystems to exceed 2GB, it still imposes a 2GB limit on individual files. I would like to get some input on how other AIX users are resolving this issue. Is there anyway to specify more than one integral file? Any suggestions will be greatly appreciated. BTW, is there a PVM (or similar) based version of Gaussian92 available? Thanks. Fred Fred Criscuolo Chemistry and Biochemistry voice: (619) 622-4113 Gensia, Inc. fax: (619) 625-4516 criscuol@gensia.com O "There's more to life than rowing.. /--/ But not much." _________________________//|/_______________________ \__________________________/_______________________/ ~~~~~~~~~ San Diego Rowing Club / est. 1888 ~~~~~~~~~~~~~~~~~ / / From gmeier@ncsa.uiuc.edu Thu Sep 29 16:11:10 1994 Received: from newton.ncsa.uiuc.edu for gmeier@ncsa.uiuc.edu by www.ccl.net (8.6.9/930601.1506) id QAA25481; Thu, 29 Sep 1994 16:03:47 -0400 Received: from [128.254.136.231] by newton.ncsa.uiuc.edu with SMTP id AA24894 (5.65a/IDA-1.4.2 for chemistry@ccl.net); Thu, 29 Sep 94 15:03:14 -0500 Message-Id: <9409292003.AA24894@newton.ncsa.uiuc.edu> X-Sender: u34065@141.142.2.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 29 Sep 1994 16:06:43 -0600 To: chemistry@ccl.net From: gmeier@ncsa.uiuc.edu (Gary Meier) Subject: Prediction of Protein Crystallinity (summary) About a week ago, I posted the following question(s) to the net and promised to summarize replies. I'm repeating the question today, as I'm still hoping to receive more information on the subject. The replies I've received to date are summarized below the question. My Original Question: Are there any algorithms, or rules of thumb, for estimating from a protein sequence the likelihood that the protein will crystallize? Can we study patterns of hydrophobic residues or some other feature(s) contained in the sequence and predict if the protein will crystallize? If so, can we suggest reasonable crystallization conditions to try? How might conditions differ if crystallization of a protein dimer is desired? Also, how might selection of a ligand for co-crystallization affect the odds of crystallization success? Is the highest affinity ligand necessarily the best choice, or are there good reasons for selecting a highly crystalline ligand, more hydrophobic ligand, etc.? Summary of Replies: (Thanks to all who responded) The first condition is that units pack identically in a lattice. This precludes diffraction study of e.g. any protein existing in a variety of native conformations in any specific state, thereby inviting the conclusion that all proteins exist in only a single native conformation in any specific state ;-). Of course, "disordered regions" are sometimes identified. I'd be delighted to be enlightened further about this issue. A second corollary of this restriction is that inter-chain "packing" forces are weak, inasmuch as strong interchain interactions on a large molecule are likely to link in "degenerate" fashion (non-uniquely?), thereby mediating a non-crystalline agglomeration. I think this problem occurs with some exposed beta-sheet structures. Note, however, that interchain attractions must be great enough to liberate heat upon crystallization sufficient to compensate for the entraopy decrease of the crystalline ordering. Thus, a delicate balance! I will look forward to other replies! Thanks, John John Reissner Pembroke State University Pembroke NC 28372 USA reissner@pembvax1.pembroke.edu vox: (910)521-6425 fax: (910)521-6649 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Just as a suggestion: there is the latest issue of Acta Cryst, Section D, Vol.50, which deals with crystallization of biological macromolecules. But I haven't in mind, if there are any articles about prediction starting from the sequence. I would think, that the only information available from the sequence is the pI and the overall/local hydrophobicity ( to be crystallized with/without detergens). Clemens -- * Clemens Vonrhein email:vonrhein@bio5.chemie.uni-freiburg.de * * * * Institut f. Org. Chemie u. Biochemie * * Albertstr.21 * * D-79104 Freiburg i.Br. (Germany) * * Tel.: 761/203-6061 FAX: 761/203-5987 * ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ I do not know if this will be useful, but Sedzik had recently published a guide on how to use variables from crystallization experiments in an optimal way. Sedzik. J., Archives of Biochemistry and Biophysics, Vol, 308, 2:342-8, 1994. The paper describes a program called DESIGN developed to address the problem of scarce resources and large amounts of protein needed for crystallization. Thomas Nittoli Dept. of Chemistry State University of NY Stony Brook, NY 11794-3400 USA Phone: (516)632-7854 FAX: (516)632-7960 Internet: nittoli@pokey.chem.sunysb.edu ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Gary Meier, Ph.D. Senior Research Computational Scientist FMC Corporation, Agricultural Chemical Group Box 8 Princeton, NJ 08543 (609) 951-3448 (gmeier@ncsa.uiuc.edu) From bryan@chem.columbia.edu Thu Sep 29 17:11:11 1994 Received: from cucbs.chem.columbia.edu for bryan@chem.columbia.edu by www.ccl.net (8.6.9/930601.1506) id QAA25614; Thu, 29 Sep 1994 16:15:00 -0400 Received: by cucbs.chem.columbia.edu id AA29665 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Thu, 29 Sep 1994 16:12:12 -0400 Date: Thu, 29 Sep 1994 16:12:12 -0400 From: netraM nayrB Message-Id: <199409292012.AA29665@cucbs.chem.columbia.edu> To: chemistry@ccl.net, CMKD344@utxvms.cc.utexas.edu, CHMORA@sn01.sncc.lsu.edu, pvarnai@lamar.colostate.edu, SATYAM@vms.cis.pitt.edu, suter@physik.unizh.ch, markus@physchem.kth.se, davide@stinch0.csmtbo.mi.cnr.it, lwalsh@aries.scs.uiuc.edu, Jeffrey.Gosper@brunel.ac.uk Subject: found MO vis. program(s) Recently I asked for a particular Molecular Orbital visualization program and any other free, ftp'able MO vis. programs. I got several very useful replies which I have encluded below. I took the liberty of modifying the replies if the information was a little out of date (like version numbers and ftp site address which have changed). I have ftp'd MOLDEN and MOPLOT2 so I know they are there but I have not had an opportunity to use them enough to list their relative merits. Thanks to all who replied, Bryan ******************************************************************** >From pvarnai@lamar.colostate.edu. I changed the MOLDEN version number below from 2.3 to 2.4. The manual describes this program as "a package for displaying molecular density. It is tuned to the Ab Initio packages GAMESS (the European version maintained by M.F. Guest et al, not the American version maintained by M.W. Schmidt et al) and GAUSSIAN. It can read all the information it needs from a GAMESS or GAUSSIAN outputfile." It runs on many Unix platforms. ******************************************************************** A program which can be of your interest: name: MOLDEN and here is what you need to do: ftp camms1.caos.kun.nl # or ftp 131.174.82.237 Name: anonymous Password: login_name_or_your_local_machine ftp> cd pub/molden ftp> binary ftp> get molden2.4.tar ftp> quit tar -xvf molden2.4.tar cd molden2.4 ******************************************************************** >From davide@stinch0.csmtbo.mi.cnr.it (author of CACAO), who apparently emailed the author of the program MOPLOT2, Dr. Lichtenberger. Here I modified David's reply by changing the ftp site and the directory where the program is to reflect what is apparently its new home. ******************************************************************** MOPLOT 2.0 ----------------------------------------------------------------------- Message 1: From: DLICHTEN@CCIT.ARIZONA.EDU I have developed a series of programs that come very close to your request. They allow virtually any Gaussian or Slater basis set and any vector coefficients, with alterations of the density matrix, etc. if you so desire. The original program MOPLOT was written in 1970 and only allowed single plane plots. This program has been available from QCPE for many years. The new MOPLOT version 2.0 does three dimensional grids as well. The output can be sent through the plotting routines of PSI88 if desired, or plotted with routines that are provided. Right now the graphics is a choice of hewlett-packard, tectronix or VGA for the PC. It is easy to incorporate other graphics. All the programs are in fortran 77 and run on both unix and vax systems without alteration. The disadvantage is that the code is probably not designed for ease of use with your wavefunctions, and you may want to alter the Gaussian subroutine to read in your wavefunctions more easily. I would be interested in having other users extend the code for their applications. If you are interested I will make the code available on a FTP site. Dennis L. Lichtenberger Professor of Chemistry Department of Chemistry University of Arizona Tucson, AZ 85721 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% PROGRAM MOPLOT2 FOR ORBITAL AND DENSITY PLOTS FROM LINEAR COMBINATIONS OF SLATER OR GAUSSIAN TYPE ORBITALS Version 2.0 June 1993 Author: Dennis L. Lichtenberger Department of Chemistry University of Arizona Tucson, Arizona 85721 email: dlichten@ccit.arizona.edu Program MOPLOT2 is extremely flexible in providing different methods for calculating and displaying the spatial distributions of orbital wavefunctions that are expressed in terms of linear combinations of Slater or Gaussian type basis functions. Although a large number of options are offered by this program, the input required for a single specific display is actually quite small. The purpose is to obtain displays that are suitbable for publication. The program provides the following output: ASCII displays of contours in planes and three-dimensional grids; contour line drawings of planes; surface projections of planes; three-dimensional surface plots; and three-dimensional grid values for display by other programs, such as PSI88. The program is actually a collection of programs written in fortran, all of which execute on SGI, CONVEX, and VAX computers. The line drawings may be in HPGL, Tektronix, or VGA formats. The HPGL formats can be converted to a variety of other formats, including postscript. The routine for Slater wavefunction input is presently consistent with the Fenske-Hall (version 5.1) format. The Gaussian functions are cartesian. Other wavefunctions may be converted to these formats, or the routines SFCALC and GFCALC may be altered for convenience. The only limitation at the present time is the lack of f orbitals, which will be added when a need develops. -------------- How to retrieve MOPLOT2 ---------- MOPLOT2 is available from the archives of Computational Chemistry List on anonymous ftp on www.ccl.net [128.146.36.5] in the directory: /pub/chemistry/software/SOURCES/FORTRAN/moplot2 If you are on the UNIX machine, it is easiest to retrieve the compressed tar archive as: % ftp www.ccl.net (or ftp 128.146.36.5) Login: anonymous Password: Your_email_address ftp> cd /pub/chemistry/software/SOURCES/FORTRAN/moplot2 ftp> binary ftp> get moplot2.tar.Z ftp> quit Then, execute command: zcat moplot2.tar.Z | tar xvof - which will unpack the archive and restore directories and files. The total size is about 6.5 Mbyte. If you do not use UNIX and do not have tar and uncompress utilities, you can retrieve files individualy. They are located under /pub/chemistry/software/SOURCES/FORTRAN/moplot2/moplot2 directory. ******************************************************************** >From Jeffrey.Gosper@brunel.ac.uk ******************************************************************** I'll summarize Jeffrey's response by saying that he (and others) are trying to get an explorer module working which takes MOPAC output and visualizes an orbital. He says this module is freely available from the net and says to find it, "do an archie search for mopac and the modules called mopac_view or something like that." They also use ChemX which is commercial software. From javito@netcom.com Thu Sep 29 20:11:12 1994 Received: from netcom17.netcom.com for javito@netcom.com by www.ccl.net (8.6.9/930601.1506) id TAA29224; Thu, 29 Sep 1994 19:46:40 -0400 Received: by netcom17.netcom.com (8.6.9/Netcom) id QAA22296; Thu, 29 Sep 1994 16:46:35 -0700 From: javito@netcom.com (James Vito) Message-Id: <199409292346.QAA22296@netcom17.netcom.com> Subject: Taxol Coordinates. To: chemistry@ccl.net Date: Thu, 29 Sep 1994 16:46:34 -0700 (PDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 160 Dear Netters, Can anyone send me some taxol coordinates. MMX MOPAC etc.... I can probably handle any format. Thanks in advance. Jim Vito javito@netcom.com From cornell@cgl.ucsf.EDU Thu Sep 29 20:13:10 1994 Received: from socrates.ucsf.EDU for cornell@cgl.ucsf.EDU by www.ccl.net (8.6.9/930601.1506) id TAA29038; Thu, 29 Sep 1994 19:23:07 -0400 Received: (from cornell@localhost) by socrates.ucsf.EDU (8.6.9/GSC4.24) id QAA04058 for chemistry@ccl.net; Thu, 29 Sep 1994 16:23:00 -0700 Date: Thu, 29 Sep 1994 16:23:00 -0700 Message-Id: <199409292323.QAA04058@socrates.ucsf.EDU> From: cornell@cgl.ucsf.edu (Wendy Cornell) To: chemistry@ccl.net Subject: charges Ton Rullmann writes: > If one decides to use ab initio theory wouldn't it make sense > to start from the perturbation theoretical approach to intermolecular > interactions, describing interactions in terms of true unimolecular > properties such as multipoles and polarizabilities? > ... text deleted... > > (The case for perturbation theory was argued in: Rullmann & van > Duijnen, Reports in Molecular Theory 1, 1 (1990). I would be very interested to see a summary of this approach posted here. It sounds like this is a molecule-based rather than an atom-based description. How many parameters ("true unimolecular properties such as multipoles and polarizabilties") would describe a molecule such as alanine? Can you even treat a molecule that is that big? Isn't this description also subject to conformational dependence? Has this model been tested for its ability to reproduce properties other than gas phase interaction energies, such as conformational energies or condensed phase properties? I'm certainly interested in hearing about other models. Even ones that aren't practical for general use in bio-simulations at the present time can provide insight into deficiencies in the working model or suggest ways to move forward towards a more complex and accurate model. ----------------------------------------------------------------------- Wendy D. Cornell Graduate Group in Biophysics Box 0446 (415) 476-2597 (phone) Department of Parmaceutical Chemistry (415) 476-0688 (fax) University of California, S.F. cornell@cgl.ucsf.edu San Francisco, CA 94143-0446 USA