From dlim@minerva.cis.yale.edu Fri Apr 8 02:55:48 1994 Received: from minerva.cis.yale.edu for dlim@minerva.cis.yale.edu by www.ccl.net (8.6.4/930601.1506) id CAA27536; Fri, 8 Apr 1994 02:17:02 -0400 Received: by minerva.cis.yale.edu (5.0/SMI-SVR4) id AA20663; Fri, 8 Apr 1994 02:17:16 +0500 From: dlim@minerva.cis.yale.edu (Dongchul Lim) Message-Id: <9404080617.AA20663@minerva.cis.yale.edu> Subject: normal coordinate calculation To: chemistry@ccl.net Date: Fri, 8 Apr 1994 02:17:15 -0400 (EDT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 14481 A number of people asked me to post a summary on normal coordinate calculations. Many chemists are interested in refinement of force constants from experimental frequencies and as well as prediction of frequencies from their force field parameters. Although the basic principle of calculating normal frequencies and coordinates have not changed much since 1960's, the efficiency of computation and user-friendliness became the major concern. A number of different algorithms for the frequency calculation appear in the literature. I'm not going to judge which one is better than the other (besides, I haven't tried all of them). A review which will appear in the April issue of Current Opinion in Structural Biology by Dr. David Case (see below) may cover this issue (?). I simply compiled the replies after some trimming. The order of the replies is absolutely based on their arrival time. I'd like to thank all who kindly replied to my question. I'll try to repost the summary if I get more information. -Dongchul Lim ==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==* >From Bill Ross (ross@cgl.ucsf.edu) ==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==* Amber contains a normal mode program. A blurb on the package as a whole is appended, followed by the beginning of the relevant section of the manual. Bill Ross AMBER 4.0 Molecular mechanics simulation programs, including source code and demos. Computer Req'ts: Fortran compiler, 25+ Mbytes disk Amber is a suite of programs for performing a variety of molecular mechanics based simulations on machines ranging from workstations to supercomputers. It is designed primarily for proteins and nucleic acids. A graphics front end is under development and should be available in spring of 1994. The 4.0 release has important new features. Free Energy: dynamically modified windows, potential of mean force, bond correction, thermodynamic integration and others. Normal modes: Langevin modes, finding transition states, new analysis tools. A new NMR-oriented energy minimization/dynamics program allows time-dependent and time-averaged constraints (e.g. simulated annealing) and direct fitting to NOESY or chemical shift data. The 'vanilla' energy minimization and dynamics program includes polarizability as an option. Distribution is in source code format, and a suite of demos is provided. The main release is in Unix and VMS; VM/CMS/MVS will have fewer demos; and the mostly standard Fortran source code can be ported elsewhere. Price: Academic & Development: $200 Industrial use: $15,000 Support: No guarantees of support. Email address & phone number provided. NMODE module Page 1 NMODE This program performs molecular mechanics calculations on proteins and nucleic acids, using first and second derivative information to find local minima, transition states, and to perform vibrational analyses. It is designed to read the prmtop and inpcrd files from the Amber suite of programs. There are accompanying programs nmanal (normal mode analysis) and lmanal (Langevin mode analysis) that use the output of these programs to compute molecular fluctuations and time correlation functions. Nmode was originally written at the University of California, Davis, by D.T. Nguyen and D.A. Case, based in part on code in the Amber 2.0 package. Major revi- sions were made at the Research Institute of Scripps Clinic by J. Kottalam and D.A. Case. M. Pique has provided valuable advice and help in porting it to many different machines. References. The second derivative routines are based on expressions used in the Consistent Force Field programs;[1] similar information is given by K.J. Miller, et al.,[2] although these expressions were not actually used in writing this code. The code also contains routines to search for tran- sition state, starting (generally) from a minimum. This pro- cedure uses a modification of the procedure of Cerjan and Miller[3] as described elsewhere.[4]` Langevin modes are analo- gous to normal modes, but in the presence of a viscous coupling to a continuum solvent. The basic ideas are presented by Lamm and Szabo,[5] and were implemented in the Amber environment by us.[6] General description: This program performs five tasks, depending on the value of the input variable ntrun (see below): ____________________ [1]S.R. Niketic and K. Rasmussen, The Consistent Force Field: A Documentation, Springer-Verlag, 1977. [2]R.J. Hinde and J. Anderson, J. Comput. Chem. 1989, 10, 63. [3]C. Cerjan and W.H. Miller, J. Chem. Phys. 1981, 75, 2800. [4]D. T. Nguyen and D. A. Case, J. Phys. Chem., 1985, 89, 4020. [5]G. Lamm and A. Szabo, J. Chem. Phys. 1986, 85, 7334. [6] J. Kottalam and D.A. Case, Biopolymers 1990, 29, 1409- 1421. _________________ (1) Perform a normal mode analysis from starting coordi- nates. Requires an input structure that has already been minimized, from process (4), below, or by some other method. In addition to the computation of normal mode frequencies, thermodynamic parameters are calcu- lated. (2) Search for transition state, starting (generally) from a minimum. See the references above for a detailed description of the method. (3) Perform a conjugate gradient minimization from the starting coordinates. This routine uses an IMSL library routine for this purpose, which is not supplied with this program. Persons who do not have access to the IMSL library should probably use the AMBER "min" program to carry out conjugate gradient minimizations. (Compile min in the double precision version for best conver- gence.) (4) Does a Newton-Raphson minimization from starting coordi- nates. A constant (tlamba) is added to the diagonal elements of the Hessian matrix to make it positive definite. Tlamba is chosen in a manner such that the step is always downhill in all directions. Whenever the change in energy is > emx or the rms of step length is > smx, the step length is scaled back repeatedly until the above two conditions are satisfied. Note that this rou- tine will not converge to a transition state. (5) Perform a langevin mode calculation, starting from a minimized structure. This option is similar to (1), but includes the viscous effects of a solvent in the calcu- lation. ==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==* From: "Don Gregory" ==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==* CHARMm has quite a good set of routines for calculating normal modes, vibrational spectra, and force-field parameter optimization of foce-constants to match the experimental IR. ==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==* From: Tom Sundius U of Helsinki ==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==* I am the author of a program for force field calculations (which of course also produces normal coordinates). It is called MOLVIB and has been included in the QCPE collection (#604, see QCPE Bull. Vol 11, Nr. 3). I include the description, which also gives some references. By the way, Gwinn's program does also use cartesian coordinates in the calculations, but had some problems with the calculation of the B-matrix, which I think were corrected by the Norwegian electron diffraction group. The classical method (so-called GF-method) is used in the Schachtschneider program, which was developed in the 60's. Shimanouchi and his coworkers in Japan developed a new program towards the end of the 60's. Description of MOLVIB: ----------------------------- Documentation for the program MOLVIB (version 6.0) Purpose: MOLVIB is a program for classical harmonic force field calculations on free and crystalline molecules. Language: Fortran 77 Hardware: VAX (VMS), IBM PC (DOS) Usage: Input instructions can be found in the supplied manual. A help file (in VAX/VMS help format) is provided. A standard test (ethane) is also included. Abstract: Normal coordinate analysis is nowadays commonly employed as an aid in the interpretation of the vibrational spectra of large molecules. In order to get meaningful results, a knowledge of the vibrational force field is necessary. Since the number of force constants grows quadratically with the number of atoms, one has to employ many approximations in the calculation of harmonic force fields even for moderately large molecules. To overcome this difficulty one can determine a force field for a set of related molecules using the so-called overlay method introduced by Snyder and Schachtschneider in the 1960's (J.H. Schachtschneider and R.G. Snyder, Spectrochim. Acta, 19 (1963) 117-168) About 1970 Gwinn developed a program for normal coordinate analysis using mass-weighted cartesian coordinates (W.D. Gwinn, J. Chem. Phys., 55, 477-481 (1971)), which eliminates the redundancy problems arising when internal valence coordinates are used, as in Wilson's GF-method. MOLVIB is based on the same fundamental idea, but differs from similar programs in many respects. The program was first described by T. Sundius, Commentat. Phys.-Math. 47, 1-66 (1977), and a more recent decription by the same author can be found in J. Mol. Struct. 218, 321-326 (1990). In addition to free molecules, crystals can also be treated. In this case, up to 50 atoms divided between 11 sub-units can be handled. All the calculations are performed using mass-weighted cartesian coordinates, instead of the conventional GF-method. This makes it possible to overcome problems with redundant coordinates. The force field is refined by a modified least squares fit of the observed normal frequencies, as described in T. Sundius, J. Mol. Spectrosc. 82, 138-151 (1980). Beginning with version 6 of the program, it is possible to change several of the maximum array dimensions, and create executables, which can handle larger molecules (or force fields). The program is user-friendly, and can be easily adopted to different force fields. It is also possible to express the force field in the CFF notation (see S.R. Niketic and Kj. Rasmussen: The Consistent Force Field: A Documentation, Lecture Notes in Chemistry, Vol. 3, Springer-Verlag (1977)). This makes it possible to use it in combination with the CFF program (or other molecular mechanics programs) for conformational analysis of flexible molecules. Accuracy: Single precision floating point. The matrix diagonalization can be performed in double precision, as shown by an alternative version of the routine EIGV. This may be advantageous on machines with small word length, especially if highly accurate eigenvectors are desired. The null frequencies, which always are printed out, can serve as a check both for machine accuracy and the validity of the input data. With single precision on a 32-bit machine, null frequencies of magnitude 1-2 cm-1 are not uncommon. Libraries: A few of the subroutines are modifications of programs previously published in books or journals, as also has been indicated in the prologues. If desired, these routines can be replaced by similar library routines (NAG or IMSL, e.g.), if such are available. Author: Tom Sundius, Department of Physics, University of Helsinki, January, 1991. ==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==* From: case@scripps.edu (David Case) ==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==* Not sure what you mean by a "normal mode computation procedure"....programs like Amber and Charmm and Discover all can compute normal modes of any molecule that their force fields cover (primarily but not exclusively biomolecules). I have a review of normal mode calculations on proteins that will appear in the April issue of Current Opinion in Structural Biology. ==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==* >From E.T.Kelsey@midge.bath.ac.uk Thu Apr 7 05:50:54 1994 ==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==* It is not clear whether you are interested in molecules or crystals; if the latter then our group uses the PARAPOCS program which can perform free energy minimisation of ionic crystal structures and calculates phonon dispersion curves. It includes the Buckingham, Lennard-Jones and Morse potential types at least and the common harmonic 3- and 4-body terms. The person to contact is Dr S.C.Parker at the University of Bath (email S.C.Parker@bath.ac.uk) if you are interested in using the program. One reference to how PARAPOCS works is: S.C.Parker and G.D.Price Advances in Solid State Chemistry, 1, 295, 1989 If you have general questions about the program I will try to help. If you want access to the code you will have to ask Dr Parker. ==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==*==* From TOMKINSON_NP%A1%UKC@ccl.net Fri Apr 8 03:56:43 1994 Received: from bit158.fisonspharm.co.uk for TOMKINSON_NP%A1%UKC@ccl.net by www.ccl.net (8.6.4/930601.1506) id DAA28391; Fri, 8 Apr 1994 03:52:16 -0400 Received: from mr.fisonspharm.co.uk by BIT158.FISONSPHARM.CO.UK (PMDF V4.2-14 #6177) id <01HAXD37YQR40006YH@BIT158.FISONSPHARM.CO.UK>; Fri, 8 Apr 1994 08:48:14 GMT Received: with PMDF-MR; Tue, 5 Apr 1994 10:50:55 GMT MR-Received: by mta IOS; Relayed; Tue, 05 Apr 1994 10:51:16 +0000 MR-Received: by mta BIT158; Relayed; Tue, 05 Apr 1994 10:50:44 +0000 Alternate-recipient: prohibited Disclose-recipients: prohibited Date: Tue, 05 Apr 1994 10:43:00 +0000 (GMT) From: "/R=UKC/R=A1/U=TOMKINSON_NP/O=Physical Chemistry/FFN=Nicholas Tomkinson/"@ccl.net Subject: Tek etc... To: chemistry%ccl.net%smtp%WPC%IOS@mr.fisonspharm.co.uk Message-id: <01HAXD3R0VR80006YH@mr.fisonspharm.co.uk> MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Posting-date: Tue, 05 Apr 1994 10:44:00 +0000 (GMT) Importance: normal Priority: normal X400-MTS-identifier: [;55050150404991/181182@UKC] A1-type: MAIL Hop-count: 2 Is it my imagination or are people responding directly to requests rather than posting to the net? Anyway, someone asked a while back about tek410* emulation for SG xterms and I wondered if anyone had any info on this. Also someone asked about WWW etc. and again I second the question. On a similar subject, does anyone know where I can get hold of a gopher client for VAX's? And does anyone have the address for the SYbyl and Biosym user group email exploders? Thanks in advance Nick Tomkinson P.S. If replying direct the address is as follows as my address seems to get scrambled when I email. tomkinson_np@ios.fisonspharm.co.uk From h.rzepa@ic.ac.uk Fri Apr 8 05:55:51 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id FAA29244; Fri, 8 Apr 1994 05:18:30 -0400 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <07940-0@punch.ic.ac.uk>; Fri, 8 Apr 1994 10:17:52 +0100 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA20111; Fri, 8 Apr 94 10:17:33 +0100 Message-Id: <9404080917.AA20111@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@sg1.cc.ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 8 Apr 1994 09:17:58 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Re: CCL:Tek etc... > Is it my imagination or are people responding directly to > requests rather than posting to the net? Anyway, someone asked > a while back about tek410* emulation for SG xterms and I > wondered if anyone had any info on this. TeemX Pericom, john stephenson or stewart leask/sales +44 (UK: 0908 265533) Also someone asked > about WWW etc. and again I second the question. On a similar > subject, does anyone know where I can get hold of a gopher > client for VAX's? Try ftp.ncsa.uiuc.edu in the Web directory. Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.02, Tel:+44 71 225 8339, Fax:+44 71 589 3869. >From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804 http://www.ch.ic.ac.uk/rzepa.html From wolpert@neon.chem.utk.edu Fri Apr 8 08:55:53 1994 Received: from neon.chem.utk.edu for wolpert@neon.chem.utk.edu by www.ccl.net (8.6.4/930601.1506) id IAA01180; Fri, 8 Apr 1994 08:38:21 -0400 Received: by neon.chem.utk.edu (4.0/1.34) id AA02067; Fri, 8 Apr 94 08:38:38 EDT Date: Fri, 8 Apr 94 08:38:38 EDT From: wolpert@neon.chem.utk.edu (Edward Wolpert) Message-Id: <9404081238.AA02067@neon.chem.utk.edu> To: tomkinson_np@ios.fisonspharm.co.uk Cc: chemistry@ccl.net In-Reply-To: <01HAXD3R0VR80006YH@mr.fisonspharm.co.uk> ("/R=UKC/R=A1/U=TOMKINSON_NP/O=Physical Chemistry/FFN=Nicholas Tomkinson/"@ccl.net) Subject: Re: CCL:Tek etc... Tom- (I'm sending this reply to the net as well.) Is it my imagination or are people responding directly to requests rather than posting to the net? Anyway, someone asked a while back about tek410* emulation for SG xterms and I wondered if anyone had any info on this. No, As the original poster of this question, I've not gotten any replies on a tek411x emulator for any xterm, to run on X11R4 or X11R5. I did get some folks who also wanted to know, for me to send replies. I'm still looking for a UNIX (Not SGI, but something that I can compile on an E&S, or RS/6000 platform) emulator for a Tek411x terminal. Normal xterm's seem to only do tek 4014. I'm looking for a non-comercial product. Also someone asked about WWW etc. and again I second the question. On a similar In short, WWW is a system to store information, and make it available to the net. It can be consider a database server. There are clients that can display the information nicely, such as Mosaic. For more information, check out the FAQ in the ftp site of rtfm.mit.edu, and go to the /pub/usenet-by-group/comp.infosystems.www directory, where they store all the FAQ's about www. subject, does anyone know where I can get hold of a gopher client for VAX's? And does anyone have the address for the SYbyl and Biosym user group email exploders? As far as a vax gopher, no. But check archie, with gopher, as the root word, and see what you can find. Also, try the privious mention ftp site; lots of good information there about the internet and computers. The Sybyl exploder's address is:sybyl@quant.chem.rpi.edu. This is not the help server, but the actual exploder, as re-quested. Virtually, Edward Wolpert --------------------------- wolpert@utk.edu | System Administrator wolpert@osti.rmt.utk.edu | Systems Programmer pa153568@utkvm1.utk.edu | Graduate Chemistry Student --------------------------- I'm sorry, but Godot isn't here today. Perhaps if you came back tomorrow... From h.rzepa@ic.ac.uk Fri Apr 8 09:57:09 1994 Received: from punch.ic.ac.uk for h.rzepa@ic.ac.uk by www.ccl.net (8.6.4/930601.1506) id JAA01659; Fri, 8 Apr 1994 09:14:49 -0400 Received: from sg1.cc.ic.ac.uk by punch.ic.ac.uk with SMTP (PP) id <14559-0@punch.ic.ac.uk>; Fri, 8 Apr 1994 14:14:04 +0100 Received: from macb.ch by cscmgb.cc.ic.ac.uk (920330.SGI/4.0) id AA17000; Fri, 8 Apr 94 14:13:47 +0100 Message-Id: <9404081313.AA17000@cscmgb.cc.ic.ac.uk> X-Sender: rzepa@sg1.cc.ic.ac.uk Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Fri, 8 Apr 1994 13:14:11 +0000 To: CHEMISTRY@ccl.net From: h.rzepa@ic.ac.uk (Henry Rzepa) (Henry Rzepa) Subject: Chemical Stereograms and Autostereograms As someone who has been a great fan of liquid crystal glasses and screens for 3D viewing of molecules, I was intrigued at the possibility of stereo chemical images for deposition on the www and gopher systems. There exist 3-4 programs for producing these things from standard (pict, gif etc) image files. I have mounted several which can be accessed >from our www home page (http://www.ch.ic.ac.uk/). No doubt if more sophisticated tools were to be developed, we could be using this much more to represent 3D chemistry. I have not seen much (any?) discussion of this in this forum. Have I missed something or is this unexplored territory? PS Stereograms need to be viewed with red/green glasses, autostereograms need only a slightly addled brain (I have to confess I cannot see the images I produced at all! Maybe I should go have a drink?) Dr Henry Rzepa, Dept. Chemistry, Imperial College, LONDON SW7 2AY; rzepa@ic.ac.uk via Eudora 2.02, Tel:+44 71 225 8339, Fax:+44 71 589 3869. >From June '94: (44) 171 584 5774, Fax: (44) 171 584 5804 http://www.ch.ic.ac.uk/rzepa.html From marshall@mcs.anl.gov Fri Apr 8 10:55:55 1994 Received: from antares.mcs.anl.gov for marshall@mcs.anl.gov by www.ccl.net (8.6.4/930601.1506) id KAA02293; Fri, 8 Apr 1994 10:24:14 -0400 Received: from mcs.anl.gov (clyde.mcs.anl.gov [140.221.11.2]) by antares.mcs.anl.gov (8.6.4/8.6.4) with ESMTP id JAA11420 for ; Fri, 8 Apr 1994 09:24:13 -0500 Message-Id: <199404081424.JAA11420@antares.mcs.anl.gov> To: chemistry@ccl.net Subject: Re: CCL:Tek etc... In-reply-to: Your message of "Fri, 08 Apr 1994 08:38:38 EDT." <9404081238.AA02067@neon.chem.utk.edu> Date: Fri, 08 Apr 1994 09:24:11 -0500 From: ""Chris Marshall (Argonne Nat. Laboratory)"" The Biosym User Group Exploder is: dibug@comp.bioz.unibas.ch Chris ********************************************************************** * __________________________________________________________________ * *| |* *| Christopher L. Marshall |* *| Research Scientist, Coal Chemistry Group |* *| |* *| Argonne National Laboratory Phone: (708) 252-4310 |* *| Building 200; Room L-121 FAX: (708) 252-9288 |* *| 9700 South Cass Avenue Internet: clmarshall@anl.gov |* *| Argonne, IL 60439-4831 (NOTE--NEW GENERAL email ADDRESS) |* *|__________________________________________________________________|* * * ********************************************************************** From noy@tci002.uibk.ac.at Fri Apr 8 12:57:37 1994 Received: from uibk.ac.at for noy@tci002.uibk.ac.at by www.ccl.net (8.6.4/930601.1506) id MAA03740; Fri, 8 Apr 1994 12:17:18 -0400 Received: from tci002.uibk.ac.at by uibk.ac.at with SMTP id AA19154 (5.65c/IDA-1.4.4 for ); Fri, 8 Apr 1994 18:17:04 +0200 Received: by tci002.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA05625; Fri, 8 Apr 1994 18:17:03 +0200 From: noy@tci002.uibk.ac.at (Teerakiat Kerdcharoen) Message-Id: <9404081617.AA05625@tci002.uibk.ac.at> Subject: Re: CCL:Chemical Stereograms and Autostereograms To: chemistry@ccl.net Date: Fri, 8 Apr 1994 18:17:02 +0200 (DFT) In-Reply-To: <9404081313.AA17000@cscmgb.cc.ic.ac.uk> from "Henry Rzepa" at Apr 8, 94 01:14:11 pm X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1926 : : As someone who has been a great fan of liquid crystal glasses and : screens for 3D viewing of molecules, I was intrigued at the possibility of : stereo chemical images for deposition on the www and gopher systems. : There exist 3-4 programs for producing these things from standard : (pict, gif etc) image files. I have mounted several which can be accessed : from our www home page (http://www.ch.ic.ac.uk/). No doubt if more : sophisticated tools were to be developed, we could be using this much : more to represent 3D chemistry. I have not seen much (any?) : discussion of this in this forum. Have I missed something or is this : unexplored territory? : : PS Stereograms need to be viewed with red/green glasses, autostereograms : need only a slightly addled brain (I have to confess I cannot see the : images I produced at all! Maybe I should go have a drink?) Dear Dr. Henry, To see the stereographic, you have to take a look inside the picture, not at the surface. The plane of the picture is in general about 20-30 cm deep inside. There is a trick to help seeing the hidden picture. Put a glass frame ( not glass for drinking ) on the picture so that you can see your shadow at the picture. Then, look at your shadow, the picture will gradually float above and be distinguishable. After that, you will be able to see it without the glass forever. sincerely, Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen (NOY) Institute of General and Inorganic and Theoretical Chemistry Innrain 52a, A-6020 Innsbruck AUSTRIA e-mail: noy@tci2.uibk.ac.at, noy@tci.uibk.ac.at, c72454@cx.uibk.ac.at : noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Bangkok ) Research : Molecular Dynamics simulations : Computer Aided Molecular/Material Designs ----------------------------------------------------------------------------- From st-amant@theory.chem.uottawa.ca Fri Apr 8 13:55:57 1994 Received: from theory.chem.uottawa.ca for st-amant@theory.chem.uottawa.ca by www.ccl.net (8.6.4/930601.1506) id NAA04694; Fri, 8 Apr 1994 13:25:51 -0400 Received: by theory.chem.uottawa.ca (AIX 3.2/UCB 5.64/4.03) id AA19173; Fri, 8 Apr 1994 13:25:41 -0400 Date: Fri, 8 Apr 1994 13:25:41 -0400 From: st-amant@theory.chem.uottawa.ca (alain st-amant) Message-Id: <9404081725.AA19173@theory.chem.uottawa.ca> To: chemistry@ccl.net Subject: Poisson's equation Hi, I was wondering if anyone out there would have a set of subroutines that solve Poisson's equation on a single atom-centred grid (i.e., i already have synthesized the density on a set of radial and angular grid points). Spherical symmetry does not exist since I've decomposed the molecule's total density into a sum of atomic contributions. Actual software would be preferred, but references to pertinent work already in the literature would be appreciated as well. Thanks, Alain St-Amant Department of Chemistry University of Ottawa ************************************************************************ the LCGTO-DFT software package DeFT may be obtained free of charge by e-mailing: request@theory.chem.uottawa.ca ************************************************************************ From dickson@zinc.chem.ucalgary.ca Fri Apr 8 15:55:58 1994 Received: from zinc.chem.ucalgary.ca for dickson@zinc.chem.ucalgary.ca by www.ccl.net (8.6.4/930601.1506) id PAA05799; Fri, 8 Apr 1994 15:16:13 -0400 From: Received: by zinc.chem.ucalgary.ca (AIX 3.2/UCB 5.64/4.03) id AA15433; Fri, 8 Apr 1994 12:57:14 -0600 Date: Fri, 8 Apr 1994 12:57:14 -0600 Message-Id: <9404081857.AA15433@zinc.chem.ucalgary.ca> To: chemistry@ccl.net Subject: Poisson equation Hi Alain! You wrote: >I was wondering if anyone out there would have a set of subroutines >that solve Poisson's equation on a single atom-centred grid (i.e., >i already have synthesized the density on a set of radial and angular >grid points). Spherical symmetry does not exist since I've decomposed >the molecule's total density into a sum of atomic contributions. Two slightly different ways of doing this are described in A. D. Becke and R. M. Dickson, JCP 89(5) 2993-2997 (1988), and B. Delley, JCP 92(1) 508-517 (1990). As far as I'm aware, there's nothing in particular to recommend one method over the other, but I don't think a detailed comparison has ever been done. I'll send you private correspondence about the availability of the software, but I thought the whole list should see this much. Ross M. Dickson, Dept. of Chemistry, Univ. of Calgary, Alberta, Canada dickson@zinc.chem.ucalgary.ca From tj@eecs.uic.edu Fri Apr 8 17:55:59 1994 Received: from pluto.eecs.uic.edu for tj@eecs.uic.edu by www.ccl.net (8.6.4/930601.1506) id RAA07225; Fri, 8 Apr 1994 17:00:21 -0400 Received: from bert.eecs.uic.edu (bert.eecs.uic.edu [128.248.167.23]) by pluto.eecs.uic.edu (8.6.4/8.6.4) with ESMTP id PAA11681; Fri, 8 Apr 1994 15:57:54 -0500 From: tj ODonnell Received: from localhost (tj@localhost) by bert.eecs.uic.edu (8.6.5/8.6.5) id QAA08864; Fri, 8 Apr 1994 16:00:24 -0500 Message-Id: <199404082100.QAA08864@bert.eecs.uic.edu> Subject: protein structure prediction To: CHEMISTRY@ccl.net Date: Fri, 8 Apr 1994 16:00:24 -0500 (CDT) Cc: tj@eecs.uic.edu (tj ODonnell) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 226 We are looking for public domain software for the prediction of secondary structure of proteins, something like the Chou and Fassman rules. Does anyone know where we can find this? Thanks, TJ O'Donnell tj@bert.eecs.uic.edu From ilya@riga.ks.uiuc.edu Fri Apr 8 18:55:59 1994 Received: from riga.ks.uiuc.edu for ilya@riga.ks.uiuc.edu by www.ccl.net (8.6.4/930601.1506) id SAA07720; Fri, 8 Apr 1994 18:06:22 -0400 Received: by riga.ks.uiuc.edu (NX5.67d/NX3.0M) id AA06158; Fri, 8 Apr 94 17:06:23 -0500 Date: Fri, 8 Apr 94 17:06:23 -0500 From: Ilya Logunov Message-Id: <9404082206.AA06158@riga.ks.uiuc.edu> Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: Chemistry@ccl.net Subject: Potential surface of excited polyenes Dear Netters, Studing potential surface of polyenes in their first excited state using CIS (configuration interaction singles) available within Gaussian I made an interesting observation. It appears that in the first excited state of polyenes, almost free rotation around both single and double bonds can be realized. In connection with this observation I have two questions. (1) Did anybody perform high level ab initio study of the polyenes potential surface in their excited state? (2) Could somebody recommend me quantum chemical program(s) in which higher (than CIS) level of CI for the excited states is incorporated? ********************************************************* Ilya Logunov Theoretical Biophysics Group Department of Chemistry and Beckman Institute University of Illinois at U-C ilya@lisboa.ks.uiuc.edu ********************************************************* From mwd@carina.cray.com Fri Apr 8 19:00:09 1994 Received: from cray.com for mwd@carina.cray.com by www.ccl.net (8.6.4/930601.1506) id SAA07844; Fri, 8 Apr 1994 18:41:39 -0400 Received: from shamu (shamu.cray.com) by cray.com (Bob mailer 1.2) id AA05400; Fri, 8 Apr 94 17:41:14 CDT Received: by shamu id AA27011; 4.1/CRI-5.4; Fri, 8 Apr 94 17:41:09 CDT From: mwd@carina.cray.com (Mark Dalton) Message-Id: <9404082241.AA27011@shamu> Subject: Protein Secondary structure prediction To: chemistry@ccl.net Date: Fri, 8 Apr 1994 17:41:05 -0500 (CDT) X-Mailer: ELM [version 2.4 PL23] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 2858 Hi! In reference to the request for information about what software is available for secondary structure prediction of proteins. 1. MacProt - is a set of programs for analyzing protein sequences for secondary structure, chain flexibility, hydropathy, helical wheels, homology and amphipathic regions. 2. NCBI package. GREASE, TGREASE - a Kyte-Doolittle hydropathicity plotting Garnier - Protein secondary structure prediction. 3. SeqSee - Science( 258:p1369): canopus.biochem.ualberta.ca A suite of programs for protein sequence analysis 4. Email server: Name : PredictProtein Organism : Protein Design Group European Biology Molecular Laboratory (EMBL) Heidelberg / Germany Type : ANALYSIS Description: Analyze a protein sequence and sends back a multiple sequence alignment performed by a weighted dynamic programming method (MaxHom) and a secondary structure prediction produced by a profile network method (PHD). Address : predictprotein@embl-heidelberg.de Contact : To report problems: predict-help@embl-heidelberg.de I have listings of other software for 3D prediction from primary and secondary structure prediction also. I am sure there is much more, but this is a place to start. I have references for papers on neural net predictions also. Thanks! Mark OTHER Related software of posible interest: Part of the MBCRR and GDE packages: mbcrr.harvard.edu PIMA is a multiple sequence alignment program that uses a dynamic programming-based pattern construction method to align a set of homologous protein sequences (Smith, RF and Smith, TF, 1992, Protein Engineering vol 5, num 1 (should be in US libraries this week; see also Smith and Smith, 1990, PNAS 87:118-122). The multiple alignment algorithm: (1) is based on a local (Smith-Waterman) rather than global (Needleman-Wunch-Sellars) dynamic programing algo- rithm; (2) aligns sequences based on the pattern of conserved sequence elements/domains common to the homologous sequences be- ing aligned; (3) represents gaps within a multiple alignment in a simple and consistent manner; (4) can employ secondary structure-dependent gap penal- ties for use in structural modelling of new protein sequences when the 3D-structure of one or more members of the se- quence family is known. -- Mark Dalton AUG-GCU-AGA-AAG H Cray Research, Inc. M A R K | Eagan, MN 55121 CH3-S-CH2-CH2-C-COOH Internet: mwd@cray.com | (612)683-3035 NH2 From KUS%SUEARN2.BITNET@mps.ohio-state.edu Fri Apr 8 12:57:35 1994 Received: from ohstpw.mps.ohio-state.edu for KUS%SUEARN2.BITNET@mps.ohio-state.edu by www.ccl.net (8.6.4/930601.1506) id MAA03612; Fri, 8 Apr 1994 12:00:48 -0400 Received: from SUEARN2.BITNET (MAILER@SUEARN2) by MPS.OHIO-STATE.EDU (PMDF V4.2-14 #5888) id <01HAXJTH3XY88WWMOH@MPS.OHIO-STATE.EDU>; Fri, 8 Apr 1994 12:00:46 EDT Date: Fri, 08 Apr 94 20:01 MSK From: Mikhail Kuzminsky -135-6388 (095) Subject: CONVEX for ab initio calculations To: Chemistry@ccl.net Message-id: <01HAXJTH3XYA8WWMOH@MPS.OHIO-STATE.EDU> Content-transfer-encoding: 7BIT Status: R Dear Netters ! CONVEX computers are wide used for computational chemistry. May somebody estimate the reliability of CONVEX C120 or CONVEX C3xxx for a case of large e scale non-empirical calculations (for example,G92 24h per day :-) ) : - how many years will succesfully work magnetic disks - how long is mean time between computer failures etc. Mikhail Kuzminsky, Institute of Organic Chemistry Russian Ac. of Sci., Moscow KUS@SUEARN2.BITNET