From mercie@cumc.cornell.edu Fri Sep 3 04:21:58 1993 Date: Fri, 3 Sep 1993 08:21:58 -0400 (EDT) From: Gustavo Mercier Subject: HONDO 8.4 on IRIS INDIGO To: chemistry@ccl.net Message-Id: Hi, Netters! I have a few questions: 1) Does anybody know how to redirect output in UNIX to write to a tape/disk through the assignment of fortran logical i/o units? In other words, what is the equivalent of the ASSIGN statement (I believe!) from Vax/Vms or FILEDEF statement in IBM/Vm/CMS in Unix? I have tried things like: setenv fort.10 / .. path ../filename setenv fort.10 $TAPE/filename 10>filename 10>&filename fort.10>filename fort.10>&filename with no success. 2) In implementing HONDO 8.4 from ChemStation in an IRIS INDIGO R4000 under IRIX 4.0.5F I have come across the following problems: a) Using a makefile for the SGI version from QCPE (i.e. HONDO7) that implements "f77 -w -G0 -static -I -I/usr/include -O -Olimit 1500 -Nl300" upon compiling module ci1.f I get an error message: Fatal Error 1: usr/lib/fcom Signal 11 Error number: 11 by eliminating the -G0 -static options the error goes away. Any ideas? b) The clock routine in HONDO 8.4 uses a C soubroutine AIXCLK to access system routines. This compiles very nicely, but upon loading with "f77 -w -G0 -static -L -L/usr/lib -I -I/usr/include -O -Olimit 1500 -o hondo" the following subroutines are listed as undefined: Error: Undefined: aixclk_ cputime_ clockx_ datimx_ dslev_ *** Error code 1 these are found in the source code if you eliminate the las "_" character, and the last routine comes from the vec.f module for vector processors. My problem is the first 4 soubroutines. Anybody has any experience loading c modules with fortran modules using the SGI loader called through f77? thanks for any help! gus mercier mercie@cumc.cornell.edu From ssidner@unmc.edu Fri Sep 3 03:55:46 1993 Date: Fri, 3 Sep 93 08:55:46 CDT From: ssidner@unmc.edu (Steve Sidner) Message-Id: <9309031355.AA08312@karplus.unmc.edu> To: chemistry@ccl.net Subject: Re: Crystal Eyes You can buy them from SGI, or you can buy them directly from Stereographics. (Cheaper I think). Stereogaphics Corp. 2171 G - E. Francisco Blvd. San Rafael, CA 94901 You need a cable, a transmitter, and a set of glasses. I would guess all three are between $US 1K and $US 2K. Steve Sidner Eppley Institute, University of Nebraska Medical Center 600 S. 42nd St., Omaha, NE, 68198-6805, U.S.A. (402) 559-4921, FAX: (402) 559-4651 ssidner@unmc.edu ssidner@unmcvm.bitnet From d3f012@pellucidar.pnl.gov Fri Sep 3 00:31:57 1993 Date: Fri, 3 Sep 93 07:31:57 -0700 From: d3f012@pellucidar.pnl.gov Subject: Acetonitrile To: chemistry@ccl.net Message-Id: <9309031431.AA16560@pellucidar.pnl.gov> Does anyone out there have any experience running MD simulations of liquid acetonitrile? I would like to hear from you. I'm also interested in other polar non-hydrogen bonding solvents if you've tried them. Thanks Mark Thompson ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. ************************************************************************** From CFCIJZER@rulgl.LeidenUniv.nl Fri Sep 3 17:44:45 1993 Date: Fri, 03 Sep 1993 16:44:45 +0100 (MET) From: CFCIJZER@rulgl.LeidenUniv.nl Subject: BIOGRAF vs QUANTA/CHARMM To: CHEMISTRY@ccl.net Message-Id: <01H2IOI1M2CI8WX6JH@rulgl.LeidenUniv.nl> Dear netters, So far we have been using BIOGRAF, quite to our satisfaction. Molecular Simulations Inc., its supplier, however, has decided to stop further development of this package and offers Quanta/ CHARMM as an alternative. I would be very much obliged to hear from those of you who are facing the same situation, and how you acted so far. Thanks, Ad IJzerman From stoutepf@chemsci1.es.dupont.com Fri Sep 3 06:02:40 1993 Message-Id: <9309031502.AA21896@chemsci1.es.dupont.com. chemsci1 chemsci1.es.dupont.com> Date: Fri, 3 Sep 1993 11:02:40 -0500 To: chemistry@ccl.net From: stoutepf@chemsci1.es.dupont.com (Pieter Stouten) Subject: re: Crystal Eyes On Fri, 3 Sep 1993 12:59 Peter Reinert wrote: >in April 1993 a crystal eyes stereo view (glasses and emitter) was on sale >for 4900,- DM (to be ordered directly from SGI). > I have a quotation of $1,800 (approx. 3060 DM) from Biosym for glasses (without emitter) dated June 17, 1993. Cheers, Pieter. Pieter Stouten, Senior Research Scientist || Computer Aided Drug Design Group || The Du Pont Merck Pharmaceutical Company || Adventures get spoiled P.O. Box 80353, Wilmington, DE 19880-0353 || by being reduced to data Phone: +1 (302) 695 3515 || -- Fax: +1 (302) 695 2813 || Poul Anderson ARA/Fax: +1 (302) 695 4324 || E-mail: stoutepf@chemsci1.es.dupont.com || E-mail: stoutepf@lldmpc.dnet.dupont.com || From mn1@helix.nih.gov Fri Sep 3 07:12:52 1993 Date: Fri, 3 Sep 93 11:12:52 -0400 From: mn1@helix.nih.gov (M. Nicklaus) Message-Id: <9309031512.AA09927@helix.nih.gov> To: CHEMISTRY@ccl.net Subject: Elementary Text on Molecular Mechanics Dear Net-Workers, We recently had a summer student here who is a senior high school student and who asked me about an introduction to molecular mechanics. Everything I could come up with, including the four volumes of "Reviews in Computational Chemistry" by Lipkowitz and Boyd, proved to be way beyond the level we were looking for (and therefore way beyond understanding). On the other hand, the basic concepts of molecular mechanics don't seem to me to be too outrageously difficult to understand (in contrast to e.g. ab initio calculations). Hence my question: Does anyone know of a VERY ELEMENTARY introductory text on molecular mechanics, preferrably in the context of drug development? I'll summarize for the net if I get useful references. Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. Lab. of Medicinal Chemistry e-mail: mn1@helix.nih.gov National Cancer Institute, NIH Phone: (301) 402-3111 Bldg 37, Rm 5B29 Fax: (301) 496-5839 Bethesda, MD 20892 ------------------------------------------------------------------------ From CLETNER@DESIRE.WRIGHT.EDU Fri Sep 3 07:48:16 1993 Date: Fri, 03 Sep 1993 12:48:16 -0500 (EST) From: CLETNER@DESIRE.WRIGHT.EDU Subject: MMP2 To: chemistry@ccl.net Message-Id: <01H2IG6D5ODE000MPD@DESIRE.WRIGHT.EDU> Hello, What is the status of MMP2? Evidently there is not a ftp site to obtain it from. This makes me think that it is no longer in the public domain. If this is the case, where can I obtain it from? Thanks Chuck Charles Letner Department of Biochem. and Mol. Bio. Wright State University Dayton, OH 45435 e-mail: cletner@desire.wright.edu From CLETNER@DESIRE.WRIGHT.EDU Fri Sep 3 08:13:44 1993 Date: Fri, 03 Sep 1993 13:13:44 -0500 (EST) From: CLETNER@DESIRE.WRIGHT.EDU Subject: MM2 To: chemistry@ccl.net Message-Id: <01H2IGZRD2LE000MPD@DESIRE.WRIGHT.EDU> Hello again, I have established that MM2 is in the public domain while MM3 and MMP2 are not. I have a copy of MM2 already. However, I have no documentation. Any suggestions of references that are specific for MM2 would be useful to me. Thanks Chuck Charles Letner Department of Biochem. and Mol. Bio. Wright State University Dayton, OH 45435 e-mail: cletner@desire.wright.edu From bak@isadora.albany.edu Fri Sep 3 10:12:52 1993 From: bak@isadora.albany.edu (Brian A. Kell) Message-Id: <9309031812.AA26976@isadora.albany.edu> Subject: Re: Crystal Eyes To: chp1aa@surrey.ac.uk (Mr Andrew D Allen) Date: Fri, 3 Sep 93 14:12:52 EDT > Does anyone know how much a set of crystal eyes would cost, for the SG Indigo? > And who to order from? You can order them directly from your local SGI salesperson. List price in the US is $1995. ------------------------------------------------------------------ Brian A. Kell Applications Support Specialist bak@biosym.com (518) 356-7934 Biosym Technologies, Inc. ------------------------------------------------------------------ From J_BROWN@uvmvax.uvm.edu Fri Sep 3 09:24:00 1993 Date: Fri, 3 Sep 1993 14:24 EST From: J_BROWN@uvmvax.uvm.edu Subject: Request catresian coordinates for Fullerenes To: chemistry@ccl.net Message-Id: <01H2IJLT34UO0028I4@uvmvax.uvm.edu> Could someone e-mail me cartesian coordinates (either experimental or theoretical) for the C-60 Fullerenes. Thanks in advance. Jay Brown From crc@iris133.biosym.com Fri Sep 3 04:56:07 1993 Date: Fri, 3 Sep 93 11:56:07 -0700 From: crc@biosym.com (Clifford Randall Cannon) Message-Id: <9309031856.AA10853@iris133.biosym.com> To: chemistry@ccl.net Subject: Re: Natural conformation of protein=global minimum? .--- | Keith MaloneyHuss wrote: | | From maloneyhuske%phvax.dnet@smithkline.com | (Keith MaloneyHuss x6083) | Thu Sep 2 21:16:08 1993 | | Is it assumed that the natural conformation of all proteins is | the free energy global minimum? If so, why? It must be at | least a local minimum, but why assume there is no possible lower | energy state? It is obviously not easily accessable or it would | be the natural configuration. Aren't there chaperones to assist | folding that determine the final conformation, and thus select | conformation based not upon absolute energy minimum criteria but | rather find a good (read very stable) local minimum which is in | the required shape for the protein's function? `--- So you will know, I am a computerist and simulationist, not a chemist. I also have asked these questions. What I think I have learned is: 1. Protein conformation at the free energy global minimum? One point is that "free energy" (so they tell me) is determined statistically by simulation, and takes account of entropy--which, for example, is greatly increased in a local minimum that is "narrow" in conformational space and therefore hard to reach in practice.. It also seems to me that seeking the global minimum is a good bet, but not a certain one. There may be many minima with practically the same energies but radically different conformations. Also, as Keith wrote, it might be impossible for the protein to reach the global minimum from the conformation in which it is sequentially constructed, and in the environment of the mitochondrion. 2. Aren't there chaperones to assist folding...? Knowing nothing about biochemistry 2-1/2 years ago, it seemed to me that there MUST be chaperones for all large proteins and com- plexes for them to fold and assemble properly. I have been told: "Sometimes but usually not." Since observation (so far) indicates that most proteins must fold by themselves, it seems to my (admit- tedly untrained) eye that simulating the processes of protein con- struction and folding simultaneously might produce better results than trying to "fold" complete sequences. Certainly many actual proteins, once denatured, will not re-fold into their natural conformations. 3. ...a good (read very stable) local minimum...required for the protein's function? Yes and no. SOME parts of the protein must be very stable; these are usually the helical and sheet regions (but a-helix to 3/10- helix conversion has been proposed as a mechanism for transmem- brane signalling). But other parts must be only weakly stable: large conformational changes are common in the active sites and are a necessary part of the proteins' activity. The naive view (which I am well qualified to state) is that the very stable sec- tions are like the supporting structure of a machine and the less stable sections are the "moving parts". I'd love (really) for my comments above to be corrected or amplified by Those Who Really Know. ________________________________________________________ The human mind treats a new idea the way the body treats a strange protein; it rejects it. - Biologist P. B. Medawar From d3f012@pellucidar.pnl.gov Fri Sep 3 12:34:20 1993 Date: Fri, 3 Sep 93 19:34:20 -0700 From: d3f012@pellucidar.pnl.gov Subject: Acetonitrile Simulations To: chemistry@ccl.net Message-Id: <9309040234.AA17253@pellucidar.pnl.gov> Thanks to the respondees of my inquiry regarding simulations of acetonitrile. The reference that was cited to me a couple of times was: Jorgensen and Briggs; Molecular Physics vol. 63, p 547 (1988). This paper outlines a 3-site model for acn (methyl hydrogens are implicit). An earlier set of papers was: 1. Bohm, et. al. Mol. Phys. vol 49, p 347 (1983) 2. Bohm, et. al. Mol. Phys. vol 51, p 761 (1984) These latter two papers apparently outline a 6-site model (methyl hydrogens are included). I have not been able to get the Bohm papers from our local technical library and they must be ordered. Since this process could take me up to 3 weeks to get the papers, do any kind souls have the parameters for Bohm's force field that they could simply send to me by email? Thanks for all the help. If any new info is sent to me, I'll post it. Mark Thompson ************************************************************************** Mark A. Thompson Sr. Research Scientist email: d3f012@pnlg.pnl.gov Molecular Science Research Center FAX : 509-375-6631 Pacific Northwest Laboratory voice: 509-375-6734 PO Box 999, Mail Stop K1-90 Richland, WA. 99352 Argus available via anonymous ftp from pnlg.pnl.gov (130.20.64.11) (in the argus directory). Download the README file first. Disclaimer: The views expressed in this message are solely my own and do not represent Battelle Memorial Institute, Pacific Northwest Laboratory, or any of its clients. **************************************************************************