From chiremv!andromeda!jeffb@uunet.UU.NET Wed Sep 8 11:02:59 1993 Date: Wed, 8 Sep 93 18:02:59 -0700 From: chiremv!andromeda!jeffb@uunet.UU.NET (Jeff Blaney) Message-Id: <9309090102.AA24434@andromeda> To: chemistry@ccl.net Subject: Re: Wanted: local optimization algorithms in C Numerical Recipes has a good chapter on optimization methods, including source code: Numerical Recipes in C: The Art of Scientific Computing, W.H. Press, S.A. Teukolsky, W.T. Vetterling, B.P. Flannery, Cambridge Univ. Press, NY, 2nd edition, 1992 ISBN 0-521-43108-5. The best conjugate gradient implementation I'm aware of is Shanno's CONMIN, which is in the public domain in Fortran (possibly available in the archives of this email list?): Shanno, D. F., Phua, K. H. "Minimization of Unconstrained Multivariate Functions", ACM Trans. Math. Softw. 1980, 6, 618-622 and Watowich, S. J., Meyer, E. S., Hagstrom, R., Josephs, R. "A Stable, Rapidly Converging Conjugate Gradient Method for Energy Minimization", J. Comp. Chem. 1988, 9, 650-661. Several people have translated CONMIN into C without trouble; I'm not aware of a generally available C version. Jeff Blaney Chiron jeffb@chiron.com From ivan@gandalf.ciam.unibo.it Wed Sep 8 11:42:35 1993 Date: Wed, 8 Sep 1993 10:42:35 +0100 From: ivan@gandalf.ciam.unibo.it (Ivan Rossi) Message-Id: <9309080942.AA13680@gandalf.ciam.unibo.it> To: CHEMISTRY@ccl.net Subject: Italian workshop on comp.chem. Workshop "Computational Chemistry on RISC Workstations" 7-8 October 1993 Bologna, Aula Magna del Dipartimento di Chimica "G. Ciamician" Via Selmi 2, BOLOGNA - Italy Official language: English Program First day: october 7, 1993 9.00 Prof. F. Bernardi (Dipartimento di Chimica "G. Ciamician", Bologna) Opening Remarks 9.30 Prof. G. Orlandi (Dipartimento di Chimica "G. Ciamician", Bologna) Spectroscopic analysis of Reaction Intermediates 10.15 Coffee Break 10.45 Prof. A. Bottoni (Dipartimento di Chimica "G. Ciamician", Bologna) Mechanisms of Thermal Reactions 11.30 Dr. M. Olivucci (Dipartimento di Chimica "G. Ciamician", Bologna) Mechanisms of Photochemical Reactions 12.15 Prof. R. Cimiraglia (Dipartimento di Chimica, Ferrara) Accurate Calculations in Ground and Electronically Excited States of Molecules through Variation-Perturbation Techniques) 13.00 Lunch 15.30 Dr. F. Zerbetto (Dipartimento di Chimica "G. Ciamician", Bologna) Electronic and Vibrational states of Fullerenes 16.30 Coffee Break 17.00 Prof. P. Palmieri (Dipartimento di Chimica-Fisica , Bologna) Molecular properties 18.00 Prof. P. Lazzeretti (Dipartimento di Chimica, Modena) Calculations of non-linear Response Properties Second day: october 8, 1993 9.30 Prof. C. Pisani (Dipartimento di Chimica, Torino) Solid State Properties 10.30 Coffee Break 11.00 Prof. J. Tomasi (Dipartimento di Chimica, Pisa) Models for Solvation 12.00 Dr. S. Iarlori ( ECSEC, Roma) Ab-initio Molecular Dynamics: Parallel Algorithms and Applications 13.00 Lunch 15.30 Prof. M.A. Robb (King's College, London) Models for Chemical Reactivity 16.30 Coffee Break 17.00 Prof. J. Gasteiger (Technical University, Munich) Synthesis Planning _______________ Ivan Rossi | Theoretical Organic Chemistry Group | Department of Chemistry "G. Ciamician" | EXPERT : someone who avoids all University of Bologna | Via Selmi 2, 40126 Bologna - Italy | the little errors, going straight | Tel. ++39-51-259495 | towards the catastrophe Fax ++39-51-259456 | e-mail ivan@gandalf.ciam.unibo.it | From tennant%hau410.uk.smithkline.com@smithkline.com Thu Sep 9 14:13:52 1993 Date: Thu, 9 Sep 1993 13:13:52 +0100 (BST) From: Mike Tennant Subject: Re: Wanted: local optimization algorithms in C To: chemistry@ccl.net Message-Id: A good source of PD optimization (and other) algorithms is in the files P_1_o_2:_F_C,C++_f_n_c and P_2_o_2:_F_C,C++_f_n_c. These can be ftped from charon.mit.edu in /pub/usenet-by-group/comp.lang.c cheers, Mike. From tristan@Kodak.COM Thu Sep 9 06:42:42 1993 Date: Thu, 9 Sep 93 10:42:42 EDT From: tristan@Kodak.COM (James Nonnemacher) Message-Id: <9309091442.AA29341@icts01.Kodak.COM> To: CHEMISTRY@ccl.net Subject: Chemical Inventory Does anyone know of software for chemical inventory and tracking other than that from MDL? Also, the person interested is currently using the Daylight chemical database software so it would be adventageous for this software to work with the Daylight software; which is currently running on and SGI Crimson workstation. From zellmer@sodium.mps.ohio-state.edu Thu Sep 9 06:24:56 1993 Date: Thu, 9 Sep 93 10:24:56 EDT From: Bob Zellmer Message-Id: <9309091424.AA02886@sodium.mps.ohio-state.edu> To: chemistry@ccl.net, zellmer@sodium.mps.ohio-state.edu Subject: Re: Global min. in protein folding > From chemistry-request@ccl.net Thu Sep 9 05:53:15 1993 > To: CHEMISTRY@ccl.net > Subject: Re: Global min. in protein folding > Date: Wed, 08 Sep 93 14:35:32 -0700 > From: avs@iris95.biosym.com > Sender: chemistry-request@ccl.net > Content-Length: 1404 > > > > > Date: Wed, 8 Sep 93 13:12:56 GMT > > From: jpj@lotus.medicine.rochester.edu (Jeffrey P. Jones) > > Subject: Global min. in protein folding > > > > > While I am not a protein folding person I have conducted an informal poll > > of protein folding folks and found that the above generalization is true. > > They all site the small proteins that refold as an example. If the protein > > cannot be refolded it is an experimental problem since it doesn't agree > > with the theory. > > > > I too, am not a protein folding person, and neither am I an > experimental chemist. However... > > IMHO, if the experimental data does not fit the theory, then the > problem should be with the theory and not the experimental data. > > I would think that *any* theory would at the least, try to explain the > existing experimental results. > > > > **************************************************** > Ajay Shah, Ph.D. > BIOSYM Technologies > avs@biosym.com > ****************************************************** > Have You Heard of the Symmetry Death of the Universe? > ****************************************************** Why does one assume that the problem is with the theory or for that matter, the experiment? They are both tools to be used together. This reasoning seems to go back to the time (even still today) when all experimentalists (I see that Dr. Shah is not) just outright dismissed any theoretical results whenever they didn't agree with their results. There have been many cases in which theory has shown experiments to be incorrect or has led the way for experimentation (just as there are many cases in which theory is not correct or just gives a rough approximation to a problem). One needs to realize what level of theory is being considered and how well it applies to the molecule under consideration. If experiment and theory don't agree then both should be looked at. One should not just assume that the theory is incorrect and try to change it to conform to some experimental results, which could also be incorrect. Bob Zellmer zellmer@sodium.mps.ohio-state.edu From ravishan@tulip.wcc.wesleyan.edu Thu Sep 9 07:08:20 1993 Date: Thu, 9 Sep 1993 11:08:20 -0400 Message-Id: <9309091508.AA16281@tulip.wcc.wesleyan.edu> From: G. Ravishanker To: chemistry@ccl.net Subject: Kabsch & Sanders program I am looking to see if a public domain version of the program discussed in Kabsch & Sanders article: Wolfgang Kabsch and Christian Sanders, Biopolymers, vol. 22, 2577-2637 exists and how one can get access to it. I did look in the program_tape directory in pdb.pdb.bnl.gov but couldn't locate anything by name. The paper discusses algorithms to recognize protein secondary structural units using hydrogen bonding scheme and is apparantly used by protein crystallographers to enable them to recognize and add the secondary structure records in Brookhaven pdb file. Any help is appreciated. 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 ryszard@MSI.COM Thu Sep 9 07:02:24 1993 Date: Thu, 9 Sep 1993 11:02:24 -0400 From: ryszard@msi.com (Ryszard Czerminski X 285) Message-Id: <9309091502.AA15955@hogan.MSI.COM> To: CHEMISTRY@ccl.net, avs@iris95.biosym.com Subject: Re: Global min. in protein folding > > Date: Wed, 8 Sep 93 13:12:56 GMT > > From: jpj@lotus.medicine.rochester.edu (Jeffrey P. Jones) > > Subject: Global min. in protein folding > > > > > While I am not a protein folding person I have conducted an informal poll > > of protein folding folks and found that the above generalization is true. > > They all site the small proteins that refold as an example. If the protein > > cannot be refolded it is an experimental problem since it doesn't agree > > with the theory. > > > > I too, am not a protein folding person, and neither am I an > experimental chemist. However... > > IMHO, if the experimental data does not fit the theory, then the > problem should be with the theory and not the experimental data. > > I would think that *any* theory would at the least, try to explain the > existing experimental results. I too, am not a protein folding person, so it seems that this leg of interesting disscussion is going out of the track, but just for the record. In my opinion "if the experimental data does not fit the theory" than there is a signal that there is something interesting going on. THIS DOES NOT MEAN NECESSERILY THAT THEORY IS WRONG (although it may as well be). See for example: (1) Copernicus (his theory at the time had lower explanatory power than well entrenched Ptolomeus theory!) (2) Einsteins general relativity. As I have learned recently early experimental confirmations of this theory where to large extend results of wishful thinking. I am sure that there are many others examples of this kind. Ryszard Czerminski Molecular Simulations ryszard@msi.com From uchjs@earth.oscs.montana.edu Thu Sep 9 04:57:07 1993 Date: Thu, 09 Sep 1993 10:57:07 MDT From: uchjs@earth.oscs.montana.edu To: CHEMISTRY@ccl.net Message-Id: <00972488.865E7AC0.4448@earth.oscs.montana.edu> Subject: Experimental ion-neutral interaction energies Hi netters, Question: Are there any computational chemists out there with an interest in obtaining experimental, gas-phase interaction energies between ions and neutrals for new systems such as peptides? Any input would be appreciated. Background: I have a high-pressure mass spectrometer that is capable of measuring gas-phase, ion-molecule equilibia like: M+ + H2O = M+(H2O) Several waters can be added. We can obtain delta-H, -S, and -G. As an example, the interaction energy between a sodium ion and the first water molecule is 24.0 kcal/mol and with the second 19.8 kcal/mol. (This technique has a long history associated with names like Kebarle and Castleman. I worked with Kebarle for a number of years.) Computational chemists used the thermodynamic data extensively in the development of potential energy surfaces and also as an experimental check for calculations on systems such as ion-hydrate clusters, M+(H2O)n, where M+ can be, for example, a metal ion, an ammonium ion, a hydronium ion, or an hydroxide ion. By using modern ionization methods, we should be able to measure equilibria for new types of ions, such as protonated peptides (and maybe proteins). These can be made to cluster with smaller molecules like water of with each other. We can also produce multiply charged metal ions. (However, we need to rebuild part of the instrument to produce such ions.) We could also study smaller molecules of atmospheric interest, like HSO4- clustering with H2O, of relevance to nucleation. Jan Sunner UCHJS@EARTH.OSCS.MONTANA.EDU From rlr@acsu.buffalo.edu Thu Sep 9 14:12:23 1993 Date: Thu, 9 Sep 1993 18:12:23 -0400 From: "Raymond L. Roskwitakski" Message-Id: <199309092212.SAA23359@autarch.acsu.buffalo.edu> To: CHEMISTRY@ccl.net Subject: Measuring void Hello We have a hole (or void) in a protein which enters into the active site. Would like to determine its size quantatively, and compare it with various substrates to decide if the substrates, at a fixed conformation are too big to enter. Has anyone made or come across a quick and dirty method without having to perform extensive docking. Ray rlr@autarch.acsu.buffalo.edu From raman@bioc01.uthscsa.edu Thu Sep 9 12:36:06 1993 From: raman@bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9309092236.AA16646@bioc01.uthscsa.edu> Subject: Re: Kabsch & Sanders program To: ravishan@swan.wesleyan.edu (G. Ravishanker) Date: Thu, 9 Sep 1993 17:36:06 -0500 (CDT) Dear Ravi > I am looking to see if a public domain version of the program discussed in > Kabsch & Sanders article: > > Wolfgang Kabsch and Christian Sanders, Biopolymers, vol. 22, > 2577-2637 The program you are looking for is called DSSP and is can be FTPed from the following site: ftp.embl-heidelberg.de Look in the pub/unix/dssp directory. You will find the executables for SPARC and SGI platforms there. I presume that the latest version is deposited there. If you need the source please contact Chris Sander at Sander@embl-heidelberg.de for a license agreement and should receive the same promptly. This is the standard for doing various secondary structure calculations with PDB file input and has many features. If you have trouble getting it, let me know. With regards -raman P.S. you can also set your gopher client to connect to the same site. -- 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 c.raman@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 JKONG@ac.dal.ca Thu Sep 9 16:42:03 1993 Date: Thu, 09 Sep 1993 19:42:03 -0300 From: JKONG@ac.dal.ca Subject: Summary: queuing system and priority To: chemistry@ccl.net Message-Id: <01H2R8FP6WTE00L65E@AC.DAL.CA> Dear netters, Last month, I sent several queries about queuing system and nice command on ibm rs/6000. Here I just give the summary of replies and what I learned from them. I hope this message would be useful to those who just got machines and are going to install NQS and NFS on them, especially ibm rs6k. When we got the two ibm rs6k's, there were several problems: (1) The original printer queues do not work very well. They do not have the features you want; they are just queues. IBM has NQS but we were asked $2,000 for it. (2) Some people are willing to run at low priority because their jobs are long and cpu-bound. But the "nice" doesn't work well. I got several replies which basically have the same complain. A recent message in this net titled "nice on AIX" states this problem very well. (3) Interactive processes(commands) are slow if there are a couple of jobs running. (4) Only two(!) loggin sessions come with each machine and again we have to pay for more($500 each). Following the suggestiong of Besler(bbesler@ouchem.chem.oakland), Max(mholtha@neon.chem.tu-berlin.be) and several other people, we installed DQS, got from anon ftp site ftp.scri.fsu.edu. Thanks to Martin's (schuetz@ips.id.ethz.ch) suggestion, I changed the system call setpriority in subroutine setlimits, which sets nice value, to setprio which set a fixed priority for the calling process. Now a job in a low priority queue always sits idle whenever there is a job in a high priority queue running in cpu. Here is a tip: do not set a priority to 127(lowest possible) because a kernal process kproc has a priority of 127. Actually, the cpu time kproc consumes(ps -Af will show) tells you exactly how much time the cpu has sit idle. I set priorities of queues from 126 to 124. This makes interactive processes always run at a way higher priority than queued jobs. No obvious slow-down for running commands is found on our 580 even when 3 jobs are running. This arrangement overcomed the problem 1, 2 and 3. With the combination of NFS and DQS the requests for loggin sessions are spreaded out and one loggin for one user in a cluster should be good enough in most time. Finnally, DQS is easy to install and fun to use. I am grateful to all the guys who replied to me! Jing From dave@carbon.chem.csiro.au Fri Sep 10 04:54:12 1993 Message-Id: <199309092353.AA17574@shark.mel.dit.csiro.au> Date: Fri, 10 Sep 93 09:54:12 EST From: (Dr.) Dave Winkler Subject: Re: Chemical inventory databases To: tristan@Kodak.COM, chemistry@ccl.net Chemical Design Ltd in Oxford (producers of Chem-X) have a new molecular and chemical reaction database package which is set up for chemical inventories (as well as storing molecular structures and chemical reactions). It links to relational databases such as Oracle so in principle should be very capable. It runs on a number of platforms including SGI (that is what I run it on) and is very well priced. Their email address is chemdesign@applelink.apple.com. 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"