From chemistry-request@www.ccl.net Fri Sep 18 07:39:37 1998 Received: from goliat.eik.bme.hu (root@[152.66.250.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA26226 Fri, 18 Sep 1998 07:39:32 -0400 (EDT) Received: from localhost (dino@localhost [127.0.0.1]) by goliat.eik.bme.hu (8.9.1/8.9.1) with SMTP id NAA22544 for ; Fri, 18 Sep 1998 13:38:42 +0200 (MET DST) Date: Fri, 18 Sep 1998 13:38:41 +0200 (MET DST) From: SZIEBERTH Denes To: chemistry@www.ccl.net Subject: software RAID 0 with g94 Message-ID: Hi everyone, Has anyone got some experience with software RAID 0 under linux? I would be interested in performance benchmarks compared to hardware RAID controllers, preferably IO heavy Gaussian 94 or other QC package run times... I'd really appreciate if someone could give some help... Denes Szieberth dino@goliat.eik.bme.hu From chemistry-request@www.ccl.net Tue Sep 22 08:55:12 1998 Received: from apsu02.apsu.edu (apsu02.apsu.edu [198.146.56.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA17677 Tue, 22 Sep 1998 08:55:12 -0400 (EDT) Received: from gostowskir.apsu.edu by APSU02.APSU.EDU (PMDF V5.1-4 #16785) with ESMTP id <01J23LK81NYO001RFI@APSU02.APSU.EDU> for chemistry@www.ccl.net; Tue, 22 Sep 1998 07:51:55 CST Date: Tue, 22 Sep 1998 07:57:43 -0500 From: Rudy Gostowski Subject: mopac internal coordinates with gamess To: CCL LIST Message-id: <01J23LK82AGY001RFI@APSU02.APSU.EDU> MIME-version: 1.0 X-Mailer: Microsoft Internet Mail 4.70.1161 Content-type: text/plain; charset=ISO-8859-1 Content-transfer-encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal I would like to use MOPAC internal coordinates as data for GAMESS. If you have an example of this please forward your input file to me. thanks, Rudy Gostowski Department of Chemistry Austin Peay State University Box 4547 Clarksville, TN 37044 931-648-7624 FAX 931-648-5996 gostowskir@apsu01.apsu.edu From chemistry-request@www.ccl.net Tue Sep 22 10:41:17 1998 Received: from dirac.cnrs-orleans.fr (dirac.cnrs-orleans.fr [163.9.6.67]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA18930 Tue, 22 Sep 1998 10:41:16 -0400 (EDT) Received: (from hinsen@localhost) by dirac.cnrs-orleans.fr (AIX4.3/UCB 8.8.8/8.7) id QAA16812; Tue, 22 Sep 1998 16:38:41 +0200 Date: Tue, 22 Sep 1998 16:38:41 +0200 Message-Id: <199809221438.QAA16812@dirac.cnrs-orleans.fr> X-Authentication-Warning: dirac.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: berriz@chasma.harvard.edu CC: chemistry@www.ccl.net In-reply-to: <199809201752.NAA28473@potato.harvard.edu> (message from Gabriel Berriz on Sun, 20 Sep 1998 13:52:43 -0400) Subject: Re: CCL:CASP vs. The Tower of Babel References: <199809201752.NAA28473@potato.harvard.edu> > *Nothing* like this happens in my current field. I'm not sure why, > but I have a few guesses. For one thing, programs are a pain to port > across systems (portability of code is not a criterion for I haven't yet met a program with serious portability problems; most people use their own programs on more than one machine, so portability is important even for the original author himself. > publication). More important, in most cases I don't want the program > just to use as a black box. On the contrary, my interest in the > program is usually in how it implements a model; I want not only to > reproduce published results, but also to tweak the conditions, and to > extend the experiments. This invariably requires that I understand That's a real problem. Writing readable and modifiable code is difficult, and requires substantial experience in software development. Few scientists have this experience, or are willing to acquire it. There is also no external incentive; programs do not figure on a publication list, much less with an indication of their quality. A typical argument for keeping the status quo is "scientists have to learn so much already, there is no time to learn software development as well." Considering that software development in computational chemistry is the equivalent of experimental techniques for the lab scientist, this is a strange point of view. Would any experimentalist be taken seriously if he publicly refused to learn the fundamentals of his techniques? I doubt it. > 5 years ago half a world away. (Again, clarity of code is, for the > most part, not a criterion for publication). So, typically I conclude Indeed. One solution might be program publishing in a similar way to paper publishing: programs would be submitted to publishers who let external referees judge the quality, including modifiability, before accepting the code for a collection of "trusted code". However, where would these referees suddenly come from? > that either I re-implement the idea from scratch, which is usually > something I can't afford, or else I drop the matter altogether. I'd like to know how many potentially good ideas were never tried because of this barrier! Working in method development myself, I encountered exactly the same problems, and finally I decided that starting from scratch was the only option. Of course I was determined to do it only once, and moreover to do it right (perhaps I am an optimist). The result of this effort is the Molecular Modeling Toolkit, available at http://starship.skyport.net/crew/hinsen/mmtk.html (for anyone, you don't even have to ask!). A few projects later, I can conclude that it was well worth the effort; I can implement new ideas very rapidly. It may not be as transparent for someone else, since the developers' guide is mostly yet-to-be-written, but that will change some day, once I manage to get a real job ;-) The essential feature of this toolkit is a library approach: there is not a "program" (read: black box), but a set of largely independent modules implementing specific techniques. For modifying or extending a particular feature or technique, there is no need to understand the rest. Most new techniques (e.g. new force fields or new integrators) can in fact be implemented without ever modifying an existing program file. -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.55.69 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@www.ccl.net Tue Sep 22 11:22:41 1998 Received: from piimsdm9.univ-mrs.fr (piimsdm9.univ-mrs.fr [194.57.196.103]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA19653 Tue, 22 Sep 1998 11:22:40 -0400 (EDT) From: olivier@piimsdm9.univ-mrs.fr Received: by piimsdm9.univ-mrs.fr (920330.SGI/920502.SGI) for chemistry@www.ccl.net id AA21947; Tue, 22 Sep 98 17:36:16 -0700 Date: Tue, 22 Sep 98 17:36:16 -0700 Message-Id: <9809230036.AA21947@piimsdm9.univ-mrs.fr> To: chemistry@www.ccl.net Subject: AIM kw in G94 Hello, i want to perform a bond order analysis using the AIM=BO keyword in g94. i got the following message in the .log ------------------------- II-1. RING POINTS ------------------------X----------Y----------Z-------------------------------- ------------------------------------------------------------------------------- Ring Cartesian Coordinates Attractors Irreparable ring damage: the gap cannot be bridged in a unique way Error termination via Lnk1e in /usr/oem/g94/l609.exe. ------------------------- Can anyone help me to solve my problem? Thanks. PPPPPPPP II II MM MM PP P II II MMM MMM PPPPPPPP II II MM M M MM _____ PP II II MM M MM | PP Ii II MM MM | | MARESCA Olivier | | PIIM - CNRS UMR 6633 | | Spectrometrie et Dynamique Moleculaire | | Campus Universitaire Saint Jerome | | Service 542 | | 13397 Marseille Cedex 20 - France | | | | Tel : +33 4.91.28.85.80 | | Fax : +33 4.91.63.65.10 | | olivier@piimsdm9.univ-mrs.fr / |_______________________________________/ From chemistry-request@www.ccl.net Tue Sep 22 14:23:20 1998 Received: from post.mail.demon.net (post-11.mail.demon.net [194.217.242.40]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA21951 Tue, 22 Sep 1998 14:23:19 -0400 (EDT) Received: from [158.152.83.101] (helo=chmqst.demon.co.uk) by post.mail.demon.net with smtp (Exim 2.03 #1) id 0zLX5C-0005AF-00 for chemistry@www.ccl.net; Tue, 22 Sep 1998 18:22:39 +0000 From: David Livingstone Organization: ChemQuest To: chemistry@www.ccl.net Date: Tue, 22 Sep 1998 10:11:04 +0100 Subject: Re: CCL:Prospectives in Drug Design Reply-to: davel@chmqst.demon.co.uk Priority: normal X-mailer: Pegasus Mail for Win32 (v3.01b) Message-Id: Hi, It is actually called "Perspectives in Drug...." > has anybody heard about the series "Prospectives in Drug Discovery and > Design" published in Kluver/Escom? Where are those paperbacks > available? The usual places, like libraries. > How many volumes do exist and what are their titles? The latest volume I have seen is 14. I should ask Kluwer or a library for the titles. Dave. ------------------------------------------------------------------ D.J. Livingstone ChemQuest Cheyney House, 19-21 Cheyney St., Steeple Morden. Herts UK SG8 0LP Phone & Fax: +44 (0)1763 852569 e-mail davel@chmqst.demon.co.uk http://www.chmqst.demon.co.uk ------------------------------------------------------------------ From chemistry-request@www.ccl.net Tue Sep 22 14:28:39 1998 Received: from mailbox2.ucsd.edu (mailbox2.ucsd.edu [132.239.1.54]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA21986 Tue, 22 Sep 1998 14:28:38 -0400 (EDT) Received: from chemcca10.ucsd.edu (chemcca10.ucsd.edu [132.239.68.250]) by mailbox2.ucsd.edu (8.8.8AS/8.6.9) with ESMTP id LAA24953; Tue, 22 Sep 1998 11:28:40 -0700 (PDT) Received: from chemcca10 (localhost [127.0.0.1]) by chemcca10.ucsd.edu (980427.SGI.8.8.8/970903.SGI.AUTOCF) via SMTP id LAA19858; Tue, 22 Sep 1998 11:28:37 -0700 (PDT) Sender: wweber@chemcca10.ucsd.edu Message-ID: <3607EC55.794B@chemcca10.ucsd.edu> Date: Tue, 22 Sep 1998 11:28:37 -0700 From: Wolfgang Weber Organization: University of California at San Diego X-Mailer: Mozilla 3.0Gold (X11; I; IRIX 6.2 IP22) To: "Márcio Cyrillo" CC: CHEMISTRY@www.ccl.net Subject: Re: CCL:Restraining dihedrals using HyperChem References: <36069DEB.B4A65628@ifi.unicamp.br> Hi Marcio, technically speaking it is no problem to add any MM type potential to a semiempirical Hamiltonian for restraint purposes. One just adds the corresponding forces to the QM forces. In fact, this is done even in "old and good MOPAC", for PM3. PM3 predicts the amide bond to be non- planar, in variance with experiment. Jimmy Stewart has therefore added a restraint potential to the related dihedral to keep the amide system planar. This is the default which can be switched off. However, I do not know what HyperChem is about and what it does. Wolfgang Márcio Cyrillo wrote: > > Dear HyperChemists, > > I would like to ask you something that I think is very strange about > HyperChem Geometry Optimization (GO) calculations. Actually I had > already asked this before but the latter support man from HyperCube (Dr. > Stravrev) did not want or did not know how to answer to my question. I > think its about time to clear this issue! I hope someone can help me. > The problem is: we read in HyperChem manual that for GO optimizations we > can restraint a variable (bond length, angle or dihedral) using a > restraing constant that adds a force field to the hamiltonian of the > system so that a potential like that of a spring can "hold" the variable > to a specific supplied value. This "Hook" constant, default value equals > 60, is set up depending on the problem, but in the manual they tell us > that it cannot be as big as we want because we would then add a > nonlinear term that would perturbate the original hamiltonian producing > artificial results. > I have the following questions: > - For molecular mechanics I understand this procedure of adding a > quadratic potential to the hamiltonian to restrain a variable, but it > seems to me as being meaningless to apply the same procedure to a > semi-empirical hamiltonian. Am I wrong? > - In mopac we can easily accomplish the restraint of a variable - > changing a digit from 1 to 0 in the z-matrix scheme. Why did not > HyperChem use the same algorithm? With MOPAC it works fine, which is > pretty different in HyperChem where it almost impossible to, in fact, > restrain the variable to the desired value. Everyone that has used my > program HyperSpin (www.ifi.unicamp.br) before, knows what I mean. > Talking about HyperSpin, I am going to release a new version soon but I > am also working on a interface that will do quite the same work but > using old and good MOPAC6. > I am looking forward to hearing from you soon, best regards, > Marcio. > -- > Marcio Cyrillo - http://www.ifi.unicamp.br/~cyrillo > email: cyrillo@ifi.unicamp.br or mcyrillo@yahoo.com > ICQ: 14059279 > Graduate Student > State University of Campinas (UNICAMP), SP, Brazil > Applied Physics Department - DFA/IFGW > room 51, phone +55 19 788 5364, fax +55 19 788 5376 > > --- > Administrivia: This message is automatically appended by the mail exploder: > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > --- -- Dr. Wolfgang Weber Dept. of Chemistry and Biochemistry University of California, San Diego La Jolla, CA 92093-0365 Phone (619) 534 3038 Fax (619) 534 7042 http://chemcca10.ucsd.edu/~wweber From chemistry-request@www.ccl.net Tue Sep 22 17:55:53 1998 Received: from mail2.one.net (mail2.one.net [206.112.192.100]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA24103 Tue, 22 Sep 1998 17:55:52 -0400 (EDT) Received: from port-47-27.access.one.net ([206.112.203.31] EHLO one.net ident: IDENT-NOT-QUERIED [port 48137]) by mail2.one.net with ESMTP id <16291-22734>; Tue, 22 Sep 1998 17:55:45 -0400 Message-ID: <36081C58.D6CAAAFE@one.net> Date: Tue, 22 Sep 1998 17:53:28 -0400 From: Ray Crawford X-Mailer: Mozilla 4.04 [en] (Win95; I) To: CHEMISTRY@www.ccl.net Subject: Help finding proteins in the PDB... References: <36069DEB.B4A65628@ifi.unicamp.br> Howdy all!!! I had a question about the contents of the PDB. I’m currently doing an examination of a macromolecular docking program and I am looking for various ligand/protein complex test cases. Ideally I would like to find two proteins which have 5-10 experimentally determined structures, each with different ligands (ie Dihydrofolate Reductase with 5-10 different experimentally determined ligands in the active site). The two examples I was thinking about were: 1.) a protein with an active-site-surface cleft such as cyclophilin A. 2.) a protein with a partially or completely enclosed pocket like the retonioc acid binding protein RXRg. So far, I have looked at two examples -- ~10 experimentally determined HIV protease complexes (which have not been deposited in the PDB) and 4 cyclophilin A complexes. The problem with the HIV protease case is that the active site is too darn symmetrical and I think that it is not a fair test of the program’s “docking” ability – there are too many “good” orientations for the ligand (i.e., the program finds plausible binding modes but they are all WAY off from the experimental binding mode). CypA, on the other hand, is a perfect example of a cleft binding site but there are only 4 structures of small, drug-like molecules experimentally determined in the PDB (and they are all dipeptides which, I might add, the program nails right on…) – I think that this example is too easy. So, my question is two-fold. Do you all think I am neglecting any important “binding modes” by limiting my examination to surface clefts and enclosed pockets, and does any one know of any proteins in the PDB (or coordinate sets you would be willing to share…) that fit these criteria? Thanks, Ray Crawford Research Associate The Procter & Gamble Co.