From raman@bioc01.uthscsa.edu Tue Jun 8 17:51:47 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9306090351.AA08014@bioc01.uthscsa.edu> Subject: X servers for PC To: chemistry@ccl.net Date: Tue, 8 Jun 1993 22:51:47 -0500 (CDT) > This has been quite a bit of buzz about X servers for the Mac, but > what about the PC? I know there a quite a few products out there, > but I'd like to poll people's experience. I'd also like to ask if there > have been any benchmarks on performance and features and compatability? There are quite a few companies that suppy X terminal emulators for the IBM compatibles. The giant in this field is NCD Inc. which in collaboration with the X consortium at MIT is trying to establish a standard for X emulation (vide supra). I have tested most of the packages available for this purpose and depending on the way you want to implement it, would recommend NCD's product. Ideally, one would purchase X terminals and use them where necessary, but their cost prohibits purchase. I am interested in setting up a private network wherein users (who have access to PC's or MAC's) would tie into our SPARC or SGI workstations and run molecular modelling programs that run under X. Whenever you are using X over the network, there is always the concern about performance and speed of graphics display. Although, in most cases, one is forced to run X over the network, a private network has the advantage of being protected from intense net-traffic and hence higher speeds of transmission. With this in mind, let us look at the following packages: 1. NCD's PC-XVIEW In order to use this, one must have already established connection with the network and must be running one of the TCP/IP software packages supported by this program. Most of the conventional ones like FTP Software's TCP/IP and SUN PC-NFS are supported. Unfortunately, the public domain NCSA TELNET is not supported at the moment. PC-XVIEW is implemented under the WINDOWS environment and is extremely easy to install and very user friendly. Software is provided to run on specific hosts (i.e. SUN, SGI, etc.) to facilitate communication between the PC and the host. There is also the option of running PC-XVIEW over an asynchronous serial line, but the maximum transmission you can achieve with this is 19.2 Kbd and I don't recommend doing this, unless there is an absolute need for it. NCD plans on increasing this to 38 Kbd, but, in all honesty I would not run an X connection under 56 Kbd. It simply is too slow!! However, if running X over a modem or serial line is your primary goal, then you should request PC-XREMOTE in addition to PC-XVIEW. In fact, there is a special PC-XREMOTE version of PC-XVIEW. Currently, NCD is the only supplier for running X via serial lines. All other companies that distribute X servers for the PC provide NCD's PC-XREMOTE as an option (extra $$ ). Overall the product performs very well and I am currently running benchmark tests on them for comparison purposes. The technical support personnel of NCD are excellent and very helpful; so is their sales. Anyone interested in the results are requested to contact me in 2 to 3 weeks time! 2. Netmanage's TCP/IP X > The manufacturer claims that this is a DLL as opposed to a TSR implementation and hence it outperforms all the other X server products in the market. Unfortunately, the company failed to provide an evaluation copy, despite many requests. I cannot say too much about the package at this juncture! If anyone has additional information on its performance, I would like to hear it. 3. QUARTERDECK'S DESKVIEW386/X The original version of the software was extremely slow, and the new one seems to have fixed some of the problems. However, it does not run under Windows 3.1 and has its own GUI. I still have not tested it fully and will reveal the results to those interested. 4. MULTIVIEW/X Implemented to work under Windows. I am evaluating the product at the moment. Sales and Tech. support are quite good. The company does provide 30 day evaluation packages. I am sure that more and more X servers are mushrooming for the PC's and as a new standard is being set by NCD and the X consortium, there is no doubt that additional ones will arise. The PC configuration that is being used to test these packages includes: 486DX, 8 Mb RAM, SVGA and 3COMM ethernet card with PC-NFS. If you have additional questions, feel free to write to me. Any comments are welcome! :) -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From dov@menora.weizmann.ac.il Wed Jun 9 12:21:00 1993 From: dov@menora.weizmann.ac.il (Dov Grobgeld) Message-Id: <9306090728.AA15025@menora.weizmann.ac.il> To: chemistry@ccl.net (Computational Chemistry List ) Subject: Re: X servers for PC Date: Wed, 9 Jun 93 10:21 +0200 Another solution, which I am at the moment am using, is to use the public domain un*x for 80X86 (X>3) called Linux. It comes with X386free, a port of the MIT X-server to 80X86. My X-server performance on my 386 DecPC with an S3 based graphics accelerator in 1024x768x256 mode is noticibly much better than the X-server performance of our IBM RS/6000, 320h. Total cost of this software solution: 0 USD/NIS/SEK/YEN/etc . (If you already have the hardware.) -- ___ ___ / o \ o \ Dov Grobgeld ( o o ) o | The Weizmann Institute of Science, Israel \ o /o o / "Where the tree of wisdom carries oranges" | | | | _| |_ _| |_ From CHALLACOMBE@BAEYER.CHEM.FSU.EDU Wed Jun 9 07:52:10 1993 Date: Wed, 9 Jun 1993 11:52:10 -0400 (EDT) From: CHALLACOMBE@BAEYER.CHEM.FSU.EDU Message-Id: <930609115210.2080128f@BAEYER.CHEM.FSU.EDU> Subject: DNA secondary structure To: CHEMISTRY@ccl.net Dear Net, I am looking for algorithms/software for the prediction of DNA secondary structure from base pair sequences and/or other parameters. Please reply to me and I will post a summary to the net if there is sufficient interest. Thanks! Matt From rpearls@hawk.dcrt.nih.gov Wed Jun 9 09:51:55 1993 Date: Wed, 9 Jun 93 13:51:55 -0400 From: rpearls@hawk.dcrt.nih.gov (Robert Pearlstein) Message-Id: <9306091751.AA23013@hawk.dcrt.nih.gov> To: CHEMISTRY@ccl.net Subject: FRODO and DNA software I have two questions concerning software that I am trying to locate: 1) Is there an SGI version of FRODO, and if so, who should I contact to obtain it? 2) Does anyone know of any programs that can build non-standard DNA conformations? I am interested in unwound backbone geometries that can be used to model intercalation, as well as the ability to generate propeller twists, tilting, and sliding deformations of the base pairs to use as starting points for minimization or dynamics. Please send responses to me, and I will share them. Thank you, Robert Pearlstein NIH rpearls@helix.nih.gov From kudchadk@ecn.purdue.edu Wed Jun 9 08:41:11 1993 Date: Wed, 9 Jun 93 13:41:11 -0500 From: kudchadk@ecn.purdue.edu (Samir Kudchadkar) Message-Id: <9306091841.AA00185@hdpe.ecn.purdue.edu> To: CHEMISTRY@ccl.net Subject: Mailing list for Molecular dynamics ? Hi netters, I am a graduate student in Chemical Eng. at Purdue, working in Molecular Dynamics Simulations. I would like to know if there are any mailing lists like this one, which deal primarily with MD simulations, esp. of polymers. Thanks in advance, - Samir Kudchadkar kudchadk@hdpe.ecn.purdue.edu From mls@wucmd.wustl.edu Wed Jun 9 10:37:16 1993 Date: Wed, 9 Jun 93 15:37:16 -0500 From: mls@wucmd.wustl.edu (Mark Smythe) Message-Id: <9306092037.AA04333@wucmd> To: chemistry@ccl.net Subject: Drug Design Dear All mike whitbeck (whitbeck@maxey.unr.edu) writes: ...(deleted parts of message) >I recall awhile back there was some traffic about 'has comp. chem. methods >ever developed a new drug ?' I no longer recall the consensus of that >conversation (or was it on the drug discovery list out of oz?). >If anyone recalls a concrete example where the calculations made the >difference tell us about it. ...(deleted parts of message) There is a recent example of rational drug design in the latest Nature (see reference below). This work was carried out primarily at the Victorian College of Pharmacy (Monash University) in Melbourne, Australia. Mark von Itzstein and his colleagues used in particular Peter Goodfords Grid etc programs in their rational drug design efforts. IMHO this is an excellent example of the use of computational chemistry as a "tool" in drug design. Though, my opinions could be considered a little biased :). Mark Mark von Itzstein, Wen-Yang Wu, Gaik B Kok, Michael S Pegg, Jeffrey C Dyason, Betty Jin, Tho Van Phan, Mark L Smythe, Hume F White, Stuart W Oliver, Peter M Colman, Joseph N Varghese, D Michael Ryan, Jacqueline M Woods, Richard C Bethell, Vanessa J Hotham, Janet M Cameron and Charles R Penn, "Rational design of potent sialidase-based inhibitors of influenza virus replication", Nature, 363, 418-423 (1993). ----------------------------------------------------------------------------- | Mark Smythe | Phone : (314) 935 4683 | | Centre for Molecular Design | Fax : (314) 935 4979 | | Washington University | E-Mail: mls@wucmd.wustl.edu | | Lopata Hall, Box 1099, One Brookings | | | Drive, St Louis, Mo, 63130 | | ----------------------------------------------------------------------------- From SATYAM@vms.cis.pitt.edu Wed Jun 9 12:37:00 1993 Date: Wed, 9 Jun 1993 17:37 EST From: SATYAM@vms.cis.pitt.edu Subject: SOFTWARE/ALGORITHMS FOR DISPLAYING PROTEINS To: CHEMISTRY@ccl.net Message-Id: <01GZ6L9SGKVKC2KBF7@vms.cis.pitt.edu> Dear Netters One of the Graduate Students in our Group is looking for Software/Algorithms which display two molecules (mostly proteins) and allows them to be rotated simultaneously in real time while displaying changing interactions between them. Even References would be welcome. He uses SGI Workstations most of the time. Please reply to me directly, if interest grow I will summarize. Thanks a lot. Satyam (satyam@vms.cis.pitt.edu) From chm6@midway.uchicago.edu Wed Jun 9 11:49:59 1993 Date: Wed, 9 Jun 93 16:49:59 CDT From: "charles h martin" Message-Id: <9306092149.AA08068@midway.uchicago.edu> To: chemistry@ccl.net Subject: COLUMBUS on SGI machines Dear Netters Here at Chicago we are thinking about purchasing Silicon Graphics Grand Challenge machine. I am a little worried about making the COLUMBUS package run on this and I was wondering if anyone has ported the COLUMBUS package to an SGI indigo or an SGI crimson and if you experienced any problems. Thanks Chuck Martin ================================================================== Charles H. Martin email: chm6@quads.uchicago.edu U.S. snail: c/o Freed Group The James Franck Institute and The Department of Chemistry The University of Chicago 5640 South Ellis Avenue Chicago, Illinois 60637 Work: (312) 702-3457 Fax: (312) 702-6853 ================================================================== From dave@carbon.chem.csiro.au Thu Jun 10 04:57:51 1993 Message-Id: <199306092357.AA24912@shark.mel.dit.csiro.au> Date: Thu, 10 Jun 93 09:57:51 EST From: (Dr.) Dave Winkler Subject: Calculations on Dawson and Keggin heteropolytungstates To: chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net Dear Netters, Has anyone had any experience in running MM or MO calculations on heteropolymetalates with Keggin or Dawson structures (e.g. the heteropolytungstate HPA-23). What level of theory is necessary to reproduce geometries, give estimates of atom charges and molecular electrostatic potential, polarizability and frontier orbitals? As these compounds are so large, are their any empirical or approximate methods which may be suitable? Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From dave@carbon.chem.csiro.au Thu Jun 10 04:52:14 1993 Message-Id: <199306092351.AA24836@shark.mel.dit.csiro.au> Date: Thu, 10 Jun 93 09:52:14 EST From: (Dr.) Dave Winkler Subject: Summary of SO/SO2/OSO2 MM parameter query To: chminf-l@iubvm.ucs.indiana.edu, chemistry@ccl.net, Dear Netters, Thank you to all who responded to my query asking for MM (particularly Sybyl) parameters for sulfones, sulfoxides and sulfonates. The following is a summary of responses. ------------------------------------------------------------------------------- Alvo Aabloo (University of Tartu, Estonia) suggested JACS 1984 106, 765-84 ------------------------------------------------------------------------------- Yoshihisa Inoue (Green Cross Corp, Japan) sent a list of sulfone and sulfoxide Sybyl parameters which he said were not properly validated yet but looked very useful. * C.2 C.2 S.o2 2 11 -2 INOUE * C.2 C.2 S.o2 1 3 2 INOUE O.3 C.2 C.3 C.2 1 -0.2 3 INOUE O.3 C.2 C.3 C.3 1 0.3 2 INOUE O.3 C.2 C.3 H 1 0.15 3 INOUE O.3 C.2 C.3 O.3 1 3 3 INOUE O.2 C.2 C.3 O.3 1 2.5 -2 INOUE S.o2 C.2 C.3 H 1 0.35 -3 INOUE * C.2 N.am S.o2 1 9 -2 INOUE C.2 C.2 S.o2 N.am 1 1 -2 INOUE C.2 C.2 S.o2 O.2 1 3 -1 INOUE C.3 C.2 S.o2 O.2 1 3 3 INOUE H C.2 S.o2 N.am 1 2 3 INOUE H C.2 S.o2 O.2 1 2 3 INOUE C.1 C.3 C.3 O.3 1 0.4 2 INOUE C.3 C.3 C.3 O.3 1 0.35 3 INOUE C.3 C.3 C.3 S.o2 1 0.25 -2 INOUE O.3 C.3 C.3 S.o2 1 1.1 -1 INOUE * C.3 C.3 O.3 1 0.12 3 INOUE(m) H C.3 O.3 S.o2 1 -2 3 INOUE C.3 C.3 S.o O.2 1 0.2 3 INOUE H C.3 S.o2 C.2 1 2 3 INOUE * C.3 S.o2 C.3 1 0.5 3 INOUE * C.3 S.o2 N.am 1 0.8 3 INOUE * C.3 S.o2 O.2 1 0.2 3 INOUE H C.3 S.o2 O.2 1 3 3 INOUE * N.am S.o2 C.3 1 2 2 INOUE C.2 N.am S.o2 C.2 1 5 2 inoue C.2 N.am S.o2 C.3 1 5 2 inoue C.2 N.am S.o2 O.2 1 3 -2 inoue C.3 N.am S.o2 C.3 1 3 3 INOUE C.3 N.am S.o2 O.2 1 3 2 INOUE H N.am S.o2 C.2 1 4 2 INOUE H N.am S.o2 C.3 1 9 2 INOUE H N.am S.o2 O.2 1 5 -2 INOUE * N.am S.o2 C.ar 1 3 2 INOUE * O.3 S.o2 C.3 1 3 1 INOUE C.2 O.3 S.o2 C.3 1 2 2 INOUE C.2 O.3 S.o2 O.2 1 1.5 -2 INOUE * O.3 S.o2 C.ar 1 3 1 INOUE ------------------------------------------------------------------------------- Govinda Rao (Vertex Pharmaceuticals, US) recommended Allinger and Kao, Tetrahedron, 32, 529, 1976 and the modification by Tai, J. Comp. Chem. 2, 161, 1981. ------------------------------------------------------------------------------- Suzanne Slayden (affiliation unknown) and Geoffery Durst (DowElanco) indicated the paper by Allinger in the June issue of J. Comp. Chem.(14(6), 655-66 1993) ------------------------------------------------------------------------------- David Doherty (MSC) pointed me to a paper by Nicholas and Hopfinger on parameterization of sulfonamides in JACS in the last few years. I haven't located it yet. ------------------------------------------------------------------------------- Tudor Oprea (Washington Univ, St. Louis) suggested using the default values which Sybyl suggests when parameters are missing. Unfortunately this does not reproduce the observed crystal conformations and the results of MO calculations. ------------------------------------------------------------------------------- Adi Treasurywala (Sterling Winthrop, USA) suggested using the S.2 and S.3 Sybyl atoms types instead of the S.o and S.o2 types. I tried this and it did not reproduce the conformational information from MO calculations and experiment ------------------------------------------------------------------------------- This has helped me considerably in my search for parameters. Unfortunately I still do not have torsional paramters for (methane) sulfonates. The C-C-O-S, C-O-S-O and C-O-S-C torsional parameters are not available. Can anyone else help out? Cheers, Dave __________________________________________________________________________ Dr. David A. Winkler Voice: 61-3-542-2244 Principal Research Scientist Fax: 61-3-543-8160 CSIRO Division of Chemicals and Polymers Private Bag 10 Clayton, Australia. "Life is what happens to you while you're making other plans" From ravishan@swan.wesleyan.edu Wed Jun 9 17:25:20 1993 Date: Wed, 9 Jun 93 21:25:20 -0400 Message-Id: <9306100125.AA20260@swan.wesleyan.edu> From: G. Ravishanker To: rpearls@hawk.dcrt.nih.gov Subject: FRODO and DNA software Robert I would like to address your second question. There is a program from Richard Lavery's lab called Jumna to do preciely what you want. You specify the helicoidal parameters and the sequence and the program produces the cartesian coordinates. I am not too sure on what you can do about the backbone torsions. The e-mail address I have for Lavery is: frors31@frors31.bitnet Good luck. Ravi **************************************************************************** * Ganesan Ravishanker Ph: (203) 344-8544 Ext. 3110 * * Coordinator of Scientific Computing, Fax:(203) 344-7960 * * Adjunct Associate Professor(Dept. of Chem.) * * Wesleyan University e-mail:ravishan@swan.wesleyan.edu * * Middletown, CT 06457. * **************************************************************************** From h9290218@HKUSUB.HKU.HK Thu Jun 10 18:22:10 1993 Date: Thu, 10 Jun 1993 10:22:10 +0800 (WST) From: h9290218%hkusub.hku.hk@OHSTVMA.ACS.OHIO-STATE.EDU Subject: subscribe To: chemistry@ccl.net Message-Id: <9306100222.AA13874@hkusub.hku.hk> Dear Sir: My name is Mr.Yau Hei Ling Danny. You can call me Danny Yau. Thank you for your kind attention. From raman@bioc01.uthscsa.edu Wed Jun 9 16:45:28 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9306100245.AA08687@bioc01.uthscsa.edu> Subject: Re: SOFTWARE/ALGORITHMS FOR DISPLAYING PROTEINS To: SATYAM@vms.cis.pitt.edu Date: Wed, 9 Jun 1993 21:45:28 -0500 (CDT) Satyam In response to another query about 2 months ago, I detailed in my posting the various programs available for molecular visualization of proteins on different platforms, including SGI. You might want to dig that up from the archives at www.ccl.net. If you have trouble finding it, let me know and I can send you a copy of the same. I am also preparing another list of programs for the same purpose and you should see it posted to the net soon! Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From raman@bioc01.uthscsa.edu Wed Jun 9 16:40:40 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9306100240.AA08675@bioc01.uthscsa.edu> Subject: Re: FRODO To: rpearls@hawk.dcrt.nih.gov (Robert Pearlstein) Date: Wed, 9 Jun 1993 21:40:40 -0500 (CDT) Robert, A I am not sure if FRODO is being distributed for SGI at the moment! You might want to contact Alwyn Jones (alwyn@xray.bmc.uu.se) about its present status. But, a program similar to FRODO, which incorporates all its features and more, called CHAIN, was maintained and updated periodically until recently by Tim Reynolds at Baylor. They have now decided, for a number of reasons, to discontinue updating it, although it will continue to be distributed in its present form. I use the program and think that it works well on the SGI! You can obtain a tar tape or let Tim FTP the program to you, after completing the license agreement! You can contact Tim at the following address: skywalker@dino.qci.bioch.bcm.tmc.edu or andrew@dino.qci.bioch.bcm.tmc.edu The program is made available free to academic and non-profit users. Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ****************************************************************************** From raman@bioc01.uthscsa.edu Wed Jun 9 16:52:32 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9306100252.AA08696@bioc01.uthscsa.edu> Subject: Re: Mailing list for Molecular dynamics ? To: kudchadk@ecn.purdue.edu (Samir Kudchadkar) Date: Wed, 9 Jun 1993 21:52:32 -0500 (CDT) Hi A mailing list was just created for this purpose and will discuss the use of the PMD (parallelized molecular dynamics algorithm) by Andreas Windemuth. This is an offshoot of his wonderful MD program and is currently being tested amongst a handful of evaluators including myself! Please watch for my posting (due very soon!!) that will explicitly give instructions for access to PMD, MD and the mailing list! Cheers -raman -- C.S.Raman raman@bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354@compuserve.com - CIS SPARC & SGI Systems raman@hermes.chpc.utexas.edu - CHPC Department of Biochemistry craman@launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ******************************************************************************