From chemistry-request@server.ccl.net Thu Feb 10 06:20:46 2000 Received: from gatekeeper2.novartis.com (gatekeeper2.novartis.com [194.191.169.74]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA18957 for ; Thu, 10 Feb 2000 06:20:42 -0500 Received: from mta3.is.chbs (mta3.novartis.com [192.37.10.59]) by gatekeeper2.novartis.com (8.9.3/8.9.3) with ESMTP id LAA05453 for ; Thu, 10 Feb 2000 11:13:21 +0100 (MET) Received: from nvchbs-s0009.is.chbs (nvchbs-s0009.is.chbs [192.37.10.78]) by mta3.is.chbs (8.9.3/8.9.3) with ESMTP id LAA11756 for ; Thu, 10 Feb 2000 11:11:58 +0100 (MET) Received: from camm1.ph.chbs (camm1.ph.chbs [147.167.227.11]) by nvchbs-s0009.is.chbs (Build 98 8.9.3/NT-8.9.3) with ESMTP id LAA02719 for ; Thu, 10 Feb 2000 11:13:28 +0100 Received: (from dietrich@localhost) by camm1.ph.chbs (8.9.3/8.9.3) id LAA06703 for chemistry@ccl.net; Thu, 10 Feb 2000 11:13:26 +0100 (MET) Date: Thu, 10 Feb 2000 11:13:26 +0100 (MET) From: Alain Dietrich Message-Id: <200002101013.LAA06703@camm1.ph.chbs> To: chemistry@ccl.net Subject: Re: Anybody agrees with me? I sincerely admire Renxia (aka Arthur) for its outstanding development effort of LigBuilder during his PhD. I profoundly regret the content of this "claim for unifying". Its either a deliberate provocation or the guy is more than naive and/or has no conscience of what History is, and how things come to birth. Anyway, the MacroModel package is "our" best in best and we still heavily use and rely on it here. Hope that we'll have the freedom to continue to play with it for a while, without asking Bill's advice. -AD ______________________________________________________________ Novartis Pharma AG Email alain.dietrich@pharma.novartis.com Alain Dietrich Tel +41 61 696 68 46 WKL-136.P.69 Fax +41 61 696 27 61 CH-4002 Basel Web http://www.novartis.com Switzerland ______________________________________________________________ From chemistry-request@server.ccl.net Thu Feb 10 08:48:53 2000 Received: from Salicet.ucd.ie (mail.ucd.ie [137.43.1.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA20578 for ; Thu, 10 Feb 2000 08:48:51 -0500 Received: from CONVERSION-DAEMON by Salicet.ucd.ie (PMDF V5.2-32 #40440) id <0FPP00C01SJQGF@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Thu, 10 Feb 2000 12:40:53 +0000 (GMT) Received: from elvira.ucd.ie ([137.43.24.26]) by Salicet.ucd.ie (PMDF V5.2-32 #40440) with SMTP id <0FPP00BHNSIKEU@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Thu, 10 Feb 2000 12:39:56 +0000 (GMT) Date: Thu, 10 Feb 2000 12:39:56 +0000 From: Laurence Cuffe Subject: Claim for unifying To: CHEMISTRY@ccl.net Message-id: <0FPP00BHOSIKEU@Salicet.ucd.ie> Organization: University College Dublin MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.01d) Content-type: text/plain; charset=US-ASCII Priority: normal I think a lot of the discussion previously in this list on a standard for output files is relevant here. As I see it chemists do a lot of different things with molecules and the diversity of programs and packages reflects this. This was brought home to me after down loading a molecular viewer program which was recommended as being good for small molecules. I was interested in a range of four atom species at the time. The program performed abysmally. It seems that for some chemists "small" is molecules in or around 10 kilo daltons. If a feature of an interface is good and intuitive it tends to be widely copied. Maybe our position as users should be to discourage the copywrighting of interface features which is one cause of the diversity in program front ends. One way of doing this might be to put some set of GUI standards in the public domain for molecular manipulation. Another might be to encourage the interchangability of file formats so that you could use your favourite editor to build molecular descriptions and then export the calculation to your favourite back end program for computation. In this respect I like jaguar because it reads many file formats for input and dislike spartan because it doesn't. I am amused by gausview which will read g94 files but flattens my g98 results like pancakes! my two cents Larry Cuffe From chemistry-request@server.ccl.net Thu Feb 10 09:53:24 2000 Received: from igw8.watson.ibm.com (igw8.watson.ibm.com [198.81.209.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA20916 for ; Thu, 10 Feb 2000 09:53:24 -0500 Received: from mailhub.watson.ibm.com (mailhub.watson.ibm.com [9.2.250.97]) by igw8.watson.ibm.com (8.9.3/8.9.3/05-14-1999) with ESMTP id IAA08038; Thu, 10 Feb 2000 08:46:05 -0500 Received: from polymer.watson.ibm.com (polymer.watson.ibm.com [9.2.194.51]) by mailhub.watson.ibm.com (8.8.7/Feb-20-98) with ESMTP id IAA07878; Thu, 10 Feb 2000 08:46:04 -0500 Received: (from rossi@localhost) by polymer.watson.ibm.com (AIX4.3/8.9.3/8.9.3/01-10-2000) id IAA26140; Thu, 10 Feb 2000 08:46:04 -0500 Message-Id: <200002101346.IAA26140@polymer.watson.ibm.com> To: Renxiao Wang cc: Computational Chemistry List Subject: Re: CCL:Anybody agrees with me? In-reply-to: Your message of Wed, 09 Feb 2000 15:43:05 -0800. Date: Thu, 10 Feb 2000 08:46:04 -0500 From: "Angelo R. Rossi" Hello: I am somewhat disappointed with the CCL coordinator for allowing a posting whose content contains intensely disparaging comments about particular software applications. Surely, there is a better and more constructive way to discuss the topic of underlying principles of application software unification without engaging innuendo. Regards, A. R. Rossi From chemistry-request@server.ccl.net Thu Feb 10 10:22:46 2000 Received: from Salicet.ucd.ie (mail.ucd.ie [137.43.1.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA21067 for ; Thu, 10 Feb 2000 10:22:45 -0500 Received: from CONVERSION-DAEMON by Salicet.ucd.ie (PMDF V5.2-32 #40440) id <0FPP00201WXQAA@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Thu, 10 Feb 2000 14:15:28 +0000 (GMT) Received: from elvira.ucd.ie ([137.43.24.26]) by Salicet.ucd.ie (PMDF V5.2-32 #40440) with SMTP id <0FPP00EKLWXPLN@Salicet.ucd.ie> for CHEMISTRY@ccl.net; Thu, 10 Feb 2000 14:15:25 +0000 (GMT) Date: Thu, 10 Feb 2000 14:15:25 +0000 From: Laurence Cuffe Subject: CCL Unifying and gausview To: CHEMISTRY@ccl.net Message-id: <0FPP00EKMWXPLN@Salicet.ucd.ie> Organization: University College Dublin MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.01d) Content-type: text/plain; charset=US-ASCII Priority: normal >> amused by gausview which will read g94 files but flattens my g98 > >results like pancakes! >I'm sure someone must working on it :-) Less I do Gaussian a disservice the new version of gaussview has this sorted and its trivial to edit the g98 output files so that the older version will read them Larry Cuffe From chemistry-request@server.ccl.net Thu Feb 10 09:06:13 2000 Received: from alchemy.yonsei.ac.kr (alchemy.yonsei.ac.kr [165.132.31.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA20681 for ; Thu, 10 Feb 2000 09:06:12 -0500 Received: from bmclab1 ([165.132.31.185]) by alchemy.yonsei.ac.kr (8.8.8H2/8.8.8) with SMTP id VAA26129 for ; Thu, 10 Feb 2000 21:58:01 +0900 (KST) Message-ID: <001701bf73c6$955de220$b91f84a5@yonsei.ac.kr> From: "=?ks_c_5601-1987?B?seggx9HBtg==?=" To: Subject: Add hydrogen to the pdb file Date: Thu, 10 Feb 2000 21:58:51 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="ks_c_5601-1987" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id JAA20682 Dear CCL members, I'm a starter of molecular modeling. Is there any program(free or demo) that can add hydrogens to the pdb file according at the specified pH? Some commercial programs like Insight II or Biopolymer in Sybyl may do this, but these programs are not available for me. I'm planning to try the Autodock 3.0 program but can't start becuase of this problem. Thanks in advance. +-----+ Kim Hanjo +----------------------------------------+ | ------------- | | Ph.D candidate student | | Bioorganic & Medicinal Chemistry Lab. | | Department of Chemistry | | Yonsei University, Seoul 120-749, Korea | | ================================================ | | Homepage : http://chem.yonsei.ac.kr/~lordmiss | | E-mail : lordmiss@alchemy.yonsei.ac.kr | +----------------------------------------------------------+ From chemistry-request@server.ccl.net Thu Feb 10 09:27:30 2000 Received: from mail.rdc3.on.home.com (ha1.rdc3.on.home.com [24.2.9.68]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA20796 for ; Thu, 10 Feb 2000 09:27:29 -0500 Received: from home.com ([24.112.43.127]) by mail.rdc3.on.home.com (InterMail v4.01.01.02 201-229-111-106) with ESMTP id <20000210131745.VDNS5662.mail.rdc3.on.home.com@home.com>; Thu, 10 Feb 2000 05:17:45 -0800 Sender: zsolt@ccl.net Message-ID: <38A2BB82.69E59728@home.com> Date: Thu, 10 Feb 2000 08:22:10 -0500 From: Zsolt Zsoldos Reply-To: zsolt@simbiosys.ca Organization: SimBioSys Inc. X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: Renxiao Wang CC: Computational Chemistry List Subject: Re: CCL:Anybody agrees with me? References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Renxiao Wang wrote: > Take the computer industry as an example. If they had not had such a > standard at the very beginning (proposed by IBM, right?), maybe today we > are using dozens of different style computers. That would be a chao! Take > MicroSoft as another example. Although they make too much money, :-) they > have done an excellent job to help "unifying" the interface of most > current softwares. Therefore a software seems less confusing when we try > to use it for the first time. Oh, you have picked the perfect examples! ;-) 1. Hardware industry was monopolized by IBM. The industry was strangled, prices fixed high until the DoJ trial broke the monopoly. THEN, the hardware industry started a fast pace advancement, prices dropped tremendously and the personal computers have flooded the market becoming available to everyone. 2. OS and desktop software industry is under Microsoft monopoly: they provide the worst quality software on the face of Earth and force people to pay a ridiculous price for it _every_ time one buys a new computer. They even made people believe, that daily or more frequent reboot and system crashes are "normal" operational procedures of a computer. They have never innovated anything but stole any good ideas and forced out of business the innovator company by predatory marketing (or simply bought the company on other occasions). IF the DoJ trial or Linux will be able to crush this monopoly, THEN the software industry will make a huge leap forward and you could witness lots of new innovations and better quality... So, do you REALLY want to see the same monopoly control (what you phrased 'standard') in the molecular modelling software industry ???? Do you want a single large corporation to stifle innovation, keep the prices high and the quality low in the name of a 'standard' ? Zsolt Zsoldos From chemistry-request@server.ccl.net Thu Feb 10 09:44:10 2000 Received: from europe.std.com (europe.std.com [199.172.62.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA20853 for ; Thu, 10 Feb 2000 09:44:09 -0500 Received: from world.std.com (root@world-f.std.com [199.172.62.5]) by europe.std.com (8.9.3/8.9.3) with ESMTP id IAA11247 for ; Thu, 10 Feb 2000 08:36:53 -0500 (EST) Received: (from jle@localhost) by world.std.com (8.9.3/8.9.3) id IAA05189 for chemistry@ccl.net; Thu, 10 Feb 2000 08:35:48 -0500 (EST) Date: Thu, 10 Feb 2000 08:35:48 -0500 (EST) From: Joe M Leonard Message-Id: <200002101335.IAA05189@world.std.com> To: chemistry@ccl.net Subject: re: code diversity (unifying, etc) Folks, I think a reasonable argument could be made for those who create chemistry codes should work together to try and create a program which can read/write files in various formats. Microsoft, it seems, has tried to lock customers in through the use of unpublished formats - if this is so, it's one "business technique" which would sorta annoy this community if people tried to use it. I also think this is not a huge-expense item. However, if one is going to talk about standardizing a GUI: 1) What non-commercial, preferrable international organization would create the standard? 2) What enforcement mechanisms would be in place to insure compliance? 3) Who is going to pay for getting the GUI of pretty much every chemistry code changed - especially if this extends to the command-line and param-files as well? 4) Is interface design going to be credited towards PhD work? Just some things to think about.l.. Joe Leonard P.S. Sorry for the low-tech mail system :-). jle@world.std.com From chemistry-request@server.ccl.net Thu Feb 10 09:50:52 2000 Received: from uldns1.unil.ch (uldns1.unil.ch [130.223.8.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA20904 for ; Thu, 10 Feb 2000 09:50:51 -0500 Received: from pcbch3207h.unil.ch ([130.223.143.63] helo=pcbch3207h ident=aborel) by uldns1.unil.ch with esmtp (Exim 2.12 #1) id 12Itsb-00019N-00; Thu, 10 Feb 2000 14:43:33 +0100 Message-ID: X-Mailer: XFMail 1.4.0 on Linux X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit MIME-Version: 1.0 In-Reply-To: <0FPP00BHOSIKEU@Salicet.ucd.ie> Date: Thu, 10 Feb 2000 14:43:33 +0100 (MET) Organization: University of Lausanne Sender: aborel@pcbch3207h From: Alain Borel To: Laurence Cuffe Subject: RE: CCL:Claim for unifying Cc: CHEMISTRY@ccl.net On 10-Feb-00 Laurence Cuffe wrote: > I think a lot of the discussion previously in this list on a standard for > output files is relevant here. > As I see it chemists do a lot of different things with molecules and > the diversity of programs and packages reflects this. This was > brought home to me after down loading a molecular viewer program > which was recommended as being good for small molecules. I was > interested in a range of four atom species at the time. The > program performed abysmally. It seems that for some chemists > "small" is molecules in or around 10 kilo daltons. > If a feature of an interface is good and intuitive it tends to be widely > copied. Maybe our position as users should be to discourage the > copywrighting of interface features which is one cause of the > diversity in program front ends. Diversity of front-ends is (I think) a good thing: what would you think if you had to use a program designed for proteins only to study an 8-atoms coordination complex? Different programs should serve different purposes IMHO... On the other hand I agree that copyrighting an interface is silly. Where would we be now if Xerox had set exclusive rights on mice/windows/etc. ? > One way of doing this might be to put some set of GUI standards > in the public domain for molecular manipulation. Possibly. And then everyone could write his own plugin to perform some specific task... sounds like a good idea to me. > Another might be > to encourage the interchangability of file formats so that you could > use your favourite editor to build molecular descriptions and then > export the calculation to your favourite back end program for > computation. In this respect I like jaguar because it reads many > file formats for input and dislike spartan because it doesn't. Define "file formats" here: structure (PDB, XYZ...)? That's what Babel is for :-) Molecular dynamics trajectories? Quantum calculation results? Usually the program includes enough documentation to transform your data into a more suitable form. If not, then maybe complaining to the vendor will bring them to change their ways (especially if the threat of losing customers becomes real enough) > I am > amused by gausview which will read g94 files but flattens my g98 > results like pancakes! I'm sure someone must working on it :-) ---------------------------------- Alain Borel Year 2000: not the 21st century Date: 10-Feb-00 Time: 14:32:28 From chemistry-request@server.ccl.net Thu Feb 10 11:21:51 2000 Received: from mtiwmhc09.worldnet.att.net (mtiwmhc09.worldnet.att.net [204.127.131.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA21405 for ; Thu, 10 Feb 2000 11:21:50 -0500 Received: from dell ([63.21.224.253]) by mtiwmhc09.worldnet.att.net (InterMail v03.02.07.07 118-134) with SMTP id <20000210151232.QMAI7877@dell>; Thu, 10 Feb 2000 15:12:32 +0000 Message-Id: <3.0.6.32.20000210071214.0098dc00@postoffice.worldnet.att.net> X-Sender: davidgallagher@postoffice.worldnet.att.net X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.6 (32) Date: Thu, 10 Feb 2000 07:12:14 -0800 To: Daniel.Tunega@itc.univie.ac.at From: David Gallagher Subject: periodic-semiempirical Cc: "chemistry@ccl.net" In-Reply-To: <38A07E54.E0A62D4A@itc.univie.ac.at> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi Daniel, MOPAC 2000 is a supported commercial semiempirical code that includes 1D, 2D and 3D periodic boundary conditions. It also includes an additional utility, MAKPOL, to assist in building crystal structures for input into MOPAC. To cope with large systems, MOPAC's linear scaling algorithm, MOZYME, enables calculations on up to tens of thousand of atoms in just hours on a laptop PC. There is a searchable MOPAC 2000 user-manual on-line at http://www.schrodinger.com/mopac2.html if you need more detailed information. Regards, David Gallagher, Fujitsu At 08:36 PM 2/8/00 +0000, Daniel.Tunega@itc.univie.ac.at wrote: > > > Dear CCL users, > > I would like to summarize semiempirical codes (free, commercial, etc.) > proposed for periodic 2D/3D systems. > > Thanks for each response. >-- > Daniel Tunega > Institute for Theoretical Chemistry > University of Vienna > Waehringerstrasse 17 > A-1090 Vienna, Austria > Phone: +43-1-4277-52754 > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Feb 10 11:22:48 2000 Received: from matavnet.hu (matavnet.hu [145.236.224.246]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA21419 for ; Thu, 10 Feb 2000 11:22:47 -0500 Received: (qmail 15213 invoked from network); 10 Feb 2000 16:15:27 +0100 Received: from line-217-80.dial.matav.net (HELO chemaxon.com) (145.236.217.80) by matavnet.hu with SMTP; 10 Feb 2000 16:15:27 +0100 Message-ID: <38A2D5AA.1A1821D2@chemaxon.com> Date: Thu, 10 Feb 2000 16:13:46 +0100 From: Ferenc Csizmadia Organization: ChemAxon X-Mailer: Mozilla 4.61 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, MOL-DIVERSITY@LISTSERV.ARIZONA.EDU, chemweb@ic.ac.uk Subject: JChem / chemical database building tool Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Please excuse multiple postings. ChemAxon is proud to announce the release of JChem 1.0.5. JChem is for creating custom chemical applications. Features: - Substructure, similarity and exact structure searching - Structure and SQL searching can be combined - Structure tables stored in relational databases - Supports the development of web, local-network or stand-alone systems. - 100% Java - User friendly interface - Portable (user selected OS, database engine, web server, web browser...) A web application developed using JChem typically consists: - Marvin Java applets / beans (drawing and displaying structures in web browsers) - JChem Class Library (structure search, retrieval and update, ...) - JChemManager (structure table creation, SDF export/import, ...) - custom HTML pages and Java servlets and/or Java Server Pages For more details, examples please follow these links: http://www.chemaxon.com/products.html http://www.jchem.com If you have - questions - ideas for development - special requirements please contact us. We are looking for distributors of JChem. Regards, Ferenc -- Dr. Ferenc Csizmadia Managing Director ChemAxon Ltd. Valyog u. 7, H-1032 Budapest, Hungary http://www.chemaxon.com T:+3620 9570988 Fax: +361 3875944 mailto:fcsiz@chemaxon.com From chemistry-request@server.ccl.net Thu Feb 10 13:36:39 2000 Received: from hecuba.chem.ksu.edu (hecuba.chem.ksu.edu [129.130.170.126]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA22288 for ; Thu, 10 Feb 2000 13:36:39 -0500 From: seabra@hecuba.chem.ksu.edu Received: (from seabra@localhost) by hecuba.chem.ksu.edu (AIX4.2/UCB 8.7/8.7) id LAA02436 for chemistry@ccl.net; Thu, 10 Feb 2000 11:31:01 -0600 (CST) Date: Thu, 10 Feb 2000 11:31:01 -0600 (CST) Message-Id: <200002101731.LAA02436@hecuba.chem.ksu.edu> To: chemistry@ccl.net Subject: Re: CCL:Anybody agrees with me? Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-MD5: t4zSoZRQn3lN5werlBe9UA== > Hello: > > I am somewhat disappointed with the CCL coordinator for allowing a > posting whose content contains intensely disparaging comments about > particular software applications. I believe CCL is a kind of "meeting point" were computational chemists can expose their ideas and opinions to discussion. In the same way the methods used are discussed, why can't certain programs be considered as well? It's good for the chemists, who can discuss the strogness and weakness of the programs, and it's good for the programmers, who can see what to improve in the next versions! Surely, that are more constructive ways of criticism and discussion, but I see no problem at all in citing the names of the programs. Gustavo Seabra. From chemistry-request@server.ccl.net Thu Feb 10 13:42:29 2000 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA22311 for ; Thu, 10 Feb 2000 13:42:28 -0500 Received: from sally.schrodinger.com (shenkin@sally.schrodinger.com [166.84.149.25]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id IAA25115; Thu, 10 Feb 2000 08:46:07 -0800 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.8/8.8.5) with ESMTP id LAA16517; Thu, 10 Feb 2000 11:46:00 -0500 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Thu, 10 Feb 2000 11:46:00 -0500 (EST) From: Peter Shenkin To: chemistry@ccl.net, Alain Dietrich Subject: Re: CCL:Anybody agrees with me? In-Reply-To: <200002101013.LAA06703@camm1.ph.chbs> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, This is a bit long-winded, so be warned. :-) I want to point out some of the issues that make it hard to define a single "best" paradigm for GUI design, and also to make some remarks about MacroModel and our new Maestro interface. First, Alain, thanks for your kind words concerning MacroModel. I think Renxia's remark concerning "why don't we have a standard" for how these programs work is, in fact, somewhat naive, for the reasons Alain pointed out. I also don't think it's that hard to learn the basic operations of a new GUI (in my experience, anyway). For the complex operations, the underlying model and capabilities of GUIs differ greatly enough so that I doubt there's enough in common to standardize. We see this even in desktop design, spreadsheets and word-processing programs, so perhaps it's not too surprising that we see it in comp. chem. GUIs as well. I greatly admire the user-friendliness of Spartan, which Renxia pointed out. This comes, in part, because it is quite deliberately spartan -- hence the name. It doesn't try to do everything. In fact, our awareness of the need for a simple interface to do the basics led to our partnership with Wavefunction that resulted in the Titan product. But in fact, my experience is that "versatility is the enemy of comprehensibility." The more an interface can do, the more difficult it is to make it user friendly. Professional modelers need to do very complicated things, indeed, and it is tough to find a model that is conceptually simple yet extensible enough to allow new things to be implemented that will only be dreamed up tomorrow. It might be that in 20 years, we'll know enough about the human mind and about how to organize not only data (nouns) but transformations (verbs) that a grand, unified user-interface paradigm will have emerged. In the meantime, we're all groping toward being as user-friendly as possible, while being as general as necessary. As Alain's remarks point out, there are lots of MacroModel users out there who know the MacroModel interface well and love it. Once you learn it, it is often easier to do complicated things with it than it is to do these things with other programs. Nevertheless, several years ago we recognized that our MacroModel interface (whose design dates back to VAX/VMS days) is not as user-friendly as it could be. We decided to develop a new interface, now called Maestro, which is being distributed right now as sort of a bare-bones preview along with MacroModel in our 7.0 distribution. For the 7.5 release, late this year, we hope to fill Maestro out sufficiently that we can retire the old MacroModel GUI. Our goals in developing Maestro were derived at least in part from many user requests we've had over the years. 1. Make the invisible visible: make the interface as self-docuemnting as possible. All options and settings should be visible or easily made visible. 2. Give it a look and feel more like contemporary GUIs, but don't give existing users something that's totally strange to them. Obviously, this is a narrow path to tread. We did go through a few prototypes and have them evaluated by exisiting users, as well as new users, in order to guide us. 3. Make it scriptable. 4. Many smaller points: use OpenGL, build an architecture that's easy to extend, etc. We will be interested in hearing back from people who have tried Maestro. Hopefully, both the Renxias and the Alains of the world will find more to like than to dislike, but whatever your impressions are, we'd like to hear your thoughts and suggestions. -P. On Thu, 10 Feb 2000, Alain Dietrich wrote: > I sincerely admire Renxia (aka Arthur) for its > outstanding development effort of LigBuilder > during his PhD. > > I profoundly regret the content of this "claim > for unifying". Its either a deliberate provocation > or the guy is more than naive and/or has no conscience > of what History is, and how things come to birth. > > Anyway, the MacroModel package is "our" best in > best and we still heavily use and rely on it here. > Hope that we'll have the freedom to continue to play > with it for a while, without asking Bill's advice. > > -AD > > > > ______________________________________________________________ > > Novartis Pharma AG Email alain.dietrich@pharma.novartis.com > Alain Dietrich Tel +41 61 696 68 46 > WKL-136.P.69 Fax +41 61 696 27 61 > CH-4002 Basel Web http://www.novartis.com > Switzerland > ______________________________________________________________ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > -- ** Whether the playing field is level depends on the coordinate system. *** ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** From chemistry-request@server.ccl.net Wed Feb 9 20:43:30 2000 Received: from teapot16.domain4.bigpond.com (teapot16.domain4.bigpond.com [139.134.5.164]) by server.ccl.net (8.8.7/8.8.7) with SMTP id UAA16743 for ; Wed, 9 Feb 2000 20:43:28 -0500 Received: from localhost (localhost [127.0.0.1]) by teapot16.domain4.bigpond.com (NTMail 3.02.13) with ESMTP id ra676667 for ; Thu, 10 Feb 2000 10:34:52 +1000 Received: from BDIP-T-014-p-55-76.tmns.net.au ([139.134.55.76]) by mail4.bigpond.com (Claudes-Configurable-MailRouter V2.7 7/413244); 10 Feb 2000 10:34:50 Message-ID: <011301bf735fa$36824e60$108b67cc@hnlsyd8> Reply-To: "Dr Huang" From: "Dr Huang" To: chemistry@ccl.net Subject: new version Polar4.1 - Electrochemical simulation and computational electrochemistry Date: Thu, 10 Feb 2000 11:38:31 +1100 I uploaded polar41c.zip to incoming directory in ccl.net. [It is available at: http://www.ccl.net/cca/software/MS-WIN95-NT/Polarograms or ftp://ftp.ccl.net/pub/chemistry/software/MS-WIN95-NT/Polarograms/] ] Polar 4.1 for Windows: Electrochemical simulation and data analysis DrHuang Pty Ltd 124 Eastern Avenue, Kingsford, Sydney, NSW 2032, Australia Phone: 61 2 96620516, 0413 008 019 mailto:polarography@bigFoot.com, showing@bigFoot.com www.electrochem.net www.DrHuang.net www.electroanal.com It analytically and digitally simulates virtually any mechanism voltammograms (polarograms) at 8 electrode geometries (planar, spherical, semi- spherical, cylindrical, semi-cylindrical, microdisc, thin film, and rotating electrodes) in over 5 techniques (linear sweep and CV, DC, normal pulse, differential pulse, and square wave voltammetries). It outputs current, resistance, conductivity and surface concentration. It also simulates effects of charge current, resistance, noise, electrolyte, stripping time, stripping potential, etc. User can type in his mechanism. It analyses any ASCII x-y data for detecting peak location, peak value, semi-derivative, derivative, intergral, semi-intergral, curve fitting, and separating overlapped peaks. It shows a tip when the user put mouse cursor over a lable. It can separate overlapped voltammograms into individuals, and extract real peaks >from voltammogram with noise and baseline. Users can compare by the theoretical peak values, analytically and digitally simulation, and choose to extract which kinetic pararmeters. Its data can be imported into other program (e.g. MS Excel). It has been successfully applied to fit experimental polarograms (voltammograms) of In(III), Cd(II), Pb(II), Tl(I), Cr(III). Zn(II), and binuclear copper complex in aqueous and non-aqueous media at mercury, solid metal and non-metal electrodes (specifically the dropping mercury, hanging mercury drop, gold, platinum and glassy carbon electrodes) by various electrochemical techniques (differential pulse, square wave, and pseudo-derivative normal pulse polarographies). It is available from the author or download from my Web site. From chemistry-request@server.ccl.net Thu Feb 10 14:05:38 2000 Received: from mail2.one.net (0@mail2.one.net [206.112.192.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA22762 for ; Thu, 10 Feb 2000 14:05:38 -0500 Received: from shell.one.net ([206.112.192.106] EHLO shell.one.net ident: IDENT-NOT-QUERIED [port 37895]) by mail2.one.net with ESMTP id <240272-28396>; Thu, 10 Feb 2000 12:58:10 -0500 Received: from localhost (iguana@localhost) by shell.one.net (8.9.3/8.9.3) with ESMTP id MAA24529; Thu, 10 Feb 2000 12:57:57 -0500 X-Authentication-Warning: shell.one.net: iguana owned process doing -bs From: Ray Crawford To: "Angelo R. Rossi" cc: Renxiao Wang , Computational Chemistry List Subject: Re: CCL:Anybody agrees with me? In-Reply-To: <200002101346.IAA26140@polymer.watson.ibm.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 10 Feb 2000 12:57:58 -0500 Howdy: Actually, I'm going to go against the grain here and post a message in support of the gentleman who challenged the various software companies to develop "standards". I find his view quite refreshing and it actually is in line with something I've been thinking about for quite a while. While I don't know if I agree with standardizing the various algorithms as he proposed, I do believe standardization would ease the frustration felt by general modelers like myself. For example, I don't think that a "standard" should be developed for, say, molecular mechanics in that every package has the same mechanics force fields. I do, however, think there should be (outside of the sometimes-obscure literature references) a documented way that all companies using the Sybyl or MMFF94 force fields should parameterize and code those particular algorithms (for example). I think standardization would also help on the file-format issue. RFC-like documents should be drafted on the standard formats such as mol2, pdb, maccs, etc. and all companies should be coerced to make various import and export formats available within their products. I think this general effort would be faciliated by the design of a testing set -- somewhat like what has been done in the PC realm with SPEC tests. With the design of such a set, all software companies would have a benchmark to which they could measure their software's quality. Does it load and save the data in this way? Can the statistical methods find this known relationship in the data? Are the descriptors computed correctly? Does this ab initio method, when coded up in our interface, give the correct answer? These are all questions that such a data set could answer. That's just my two cents worth... However, I must say that since I have apparently suffered frustrations similar to those of Renxiao, my bank has a whole lot more than those two cents in it... I also find it humorous that when some one posts a far out message like the one about the rockets destroying our ecosystem, nobody makes a peep (outside of the one by the list admin)... However, when some one raises a relevant issue in an intellectual context that affects the daily opperations of us all, people move to defame his ideas and his character. This is quite interesting. Thank you, Jan, for "letting such a message through". Ray Crawford. On Thu, 10 Feb 2000, Angelo R. Rossi wrote: > > Hello: > > I am somewhat disappointed with the CCL coordinator for allowing a > posting whose content contains intensely disparaging comments about > particular software applications. > > Surely, there is a better and more constructive way to discuss the > topic of underlying principles of application software unification > without engaging innuendo. > > Regards, > > A. R. Rossi > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Thu Feb 10 15:11:44 2000 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA23473 for ; Thu, 10 Feb 2000 15:11:43 -0500 Received: from tc.cornell.edu (LIGAND.TC.CORNELL.EDU [128.84.20.182]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with ESMTP id OAA16970 for ; Thu, 10 Feb 2000 14:04:19 -0500 Sender: richard@tc.cornell.edu Message-ID: <38A30AB1.68E11745@tc.cornell.edu> Date: Thu, 10 Feb 2000 14:00:01 -0500 From: Richard Gillilan X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Anybody agrees with me? References: <38A2BB82.69E59728@home.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit > So, do you REALLY want to see the same monopoly control (what you phrased > 'standard') in the molecular modelling software industry ???? > Do you want a single large corporation to stifle innovation, keep the prices high > and the quality low in the name of a 'standard' ? > > Zsolt Zsoldos Does anyone know what share of the market is held by MSI now? I'll bet it's huge. Richard Gillilan From chemistry-request@server.ccl.net Thu Feb 10 15:29:07 2000 Received: from mserv3.dl.ac.uk (root@mserv3.dl.ac.uk [148.79.80.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA23629 for ; Thu, 10 Feb 2000 15:29:06 -0500 Received: from dl.ac.uk (tca8.dl.ac.uk [193.62.112.106]) by mserv3.dl.ac.uk (8.9.3/8.9.3/[ref postmaster@dl.ac.uk]) with ESMTP id TAA08137 for ; Thu, 10 Feb 2000 19:22:32 GMT Sender: H.J.J.VanDam@dl.ac.uk Message-ID: <38A30D09.1432AC54@dl.ac.uk> Date: Thu, 10 Feb 2000 19:10:02 +0000 From: Huub van Dam Organization: CCLRC Daresbury Laboratory X-Mailer: Mozilla 4.05 [en] (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: Anybody agrees with me? References: <38A2BB82.69E59728@home.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Zsolt Zsoldos wrote: > Oh, you have picked the perfect examples! ;-) > > 1. Hardware industry was monopolized by IBM. The industry was strangled, > prices fixed high until the DoJ trial broke the monopoly. THEN, the hardware > industry started a fast pace advancement, prices dropped tremendously and > the personal computers have flooded the market becoming available to everyone. > > 2. OS and desktop software industry is under Microsoft monopoly: they provide > the worst quality software on the face of Earth and force people to pay a ridiculous > price for it _every_ time one buys a new computer. They even made people believe, > that daily or more frequent reboot and system crashes are "normal" operational > procedures of a computer. They have never innovated anything but stole any good > ideas and forced out of business the innovator company by predatory marketing > (or simply bought the company on other occasions). IF the DoJ trial or Linux > will be able to crush this monopoly, THEN the software industry will make a > huge leap forward and you could witness lots of new innovations and better quality... > > So, do you REALLY want to see the same monopoly control (what you phrased > 'standard') in the molecular modelling software industry ???? > Do you want a single large corporation to stifle innovation, keep the prices high > and the quality low in the name of a 'standard' ? I believe we are suffering from some confusion about terms. I think unification can be obtained by at least 2 ways:1) Domination. The IBM and Microsoft examples fall in this category. By simply crushing all the alternatives only 1 approach remains accessable to the ordinary people. The result is not necessarily the best one as Zsolt has pointed out. 2) Standardisation. With standardisation I mean that a representative part of the community active in the particular field meets to write a specification of how certain things should be done. The resulting document should ideally be accessible to everyone so that everyone can write software that meets the standard. Of course one may program additional features that extend beyond the standard as long as they don't lead to conflicts with the standard. Good examples are probably the standard C library, the SMTP standard that defines the email protocol, and HTML. On the other hand Windoze is not a standard operating system (even though most people use it), because there is no publicly accessible specification agreed on by a representative part of all operating system developers. Of course there is no requirement to write software that conforms to a standard, but you may miss the benefits of software components that are already available. Also, one should not try to standardise everything. To avoid cripling innovation and the high costs of frequent standard revisions one should only standardise those things for which there is sufficient experience to forsee the implications of the choices that have to be made. The point remains that in chemistry there are (I believe) quite a few concepts where we have a clear idea of what we are talking about. However, when it comes to representing them in software it doesn't often happen that people get together to agree on an acceptable way of how to do that. This may well be an undesirable situation. Take the example of every day street traffic. In principle it doesn't really matter whether you drive on the right or the left side of the road. Most countries though have chosen a side for the simple reason that in modern traffic any of the choices is to be much preferred over not making a choice at all. As chemistry related software becomes more of an industry every day it may well be best to make a few choices. Huub -- ======================================================================== Huub van Dam E-mail: h.j.j.vandam@dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603362 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD ======================================================================== From chemistry-request@server.ccl.net Thu Feb 10 17:58:55 2000 Received: from rzusuntk.unizh.ch (rzumail2.unizh.ch [130.60.128.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA24685 for ; Thu, 10 Feb 2000 17:58:55 -0500 Received: [from zisgi.unizh.ch (zisgi.unizh.ch [130.60.19.17]) by rzusuntk.unizh.ch (8.8.5/SMI-5.34) with ESMTP id WAA06988 for ; Thu, 10 Feb 2000 22:51:32 +0100 (MET)] Date: Thu, 10 Feb 2000 22:51:33 +0100 From: "Dr. Peter Burger" To: CHEMISTRY@ccl.net Subject: CCL:Anybody agrees with me? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I agree - just think about it - that is the reason why X11 was invented. I guess it will not change since too many programs are around of which I find Spartan very intuitive & comfortable as well. But well then for instance in the PC versions of it there is max 6-coordination possible. which may leave me alone being an inorganic chemist who has to deal with higher coordination numbers also. Anyways, what _really_ annoys me is the number of different file formats for cartesian and internal coordinates (46 or so in Babel) - why did every programmer have to reinvent the wheel!! Babel albeit being nice also has its drawbacks. Regards, Peter --------------------------------------- Peter Burger Anorg.-chem. Institut University of Zuerich chburger@aci.unizh.ch From chemistry-request@server.ccl.net Thu Feb 10 19:21:30 2000 Received: from ce.fis.unam.mx (ce.fis.unam.mx [132.248.33.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA25181 for ; Thu, 10 Feb 2000 19:21:29 -0500 Received: (from ramon@localhost) by ce.fis.unam.mx (8.8.8/8.7.1) id RAA04488 for chemistry@ccl.net; Thu, 10 Feb 2000 17:50:59 -0800 (PST) From: Ramon Garduno Message-Id: <200002110150.RAA04488@ce.fis.unam.mx> Subject: POSTSCRIPT VIEWER...HELP!!! To: chemistry@ccl.net Date: Thu, 10 Feb 2000 17:50:59 PST X-Mailer: Elm [revision: 212.2] Dear CCLers: I know I am going to get flamed for asking a question in a non related CCL topic, but I have tried to install GHOSTVIEW in my SGI Octane, and I can do it right. I need to edit a few nice protein folding pictures from a Postscript file so that I can print them in a color printer. The only postscript viewer that can allow me to do it is GhostView Version 3.5.8, which in turn needs access to files and library named Xaw3d. I have managed to get the *.c and *.h for Xaw3d; however, I still need to link the gv-3.5.8 *.o to a library named libXaw3d.a & libXaw3d.so which are not available from the SGI Freeware WWW site. I know you are going to tell me that I should use "ar" to create the library, but in order to compile the *.c from Xaw3d I need to do a lot of work that I do not feel confident to do without screwing up. This step requires to compile properly many files for the X11 enviroment which are different to the Xaw found in it. Thus, I would like to know if any one of you (kind souls) has done this before and is willing to share the secrets, or better yet, if by any chance someone has both libraries installed in a SGI IRIX6.5, could you allow me to use them?.... Much obliged. Ramon -- "There are so many ways.... There is so little time...." "Hay tantos caminos..... Pero, hay tan poco tiempo....." ___________________________________________________________________________ Dr. Ramon Garduno-Juarez Research Professor in Biophysics CENTRO DE CIENCIAS FISICAS | EMAIL: ramon@ce.fis.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | Apdo. Postal 48-3 | VOICE: +52(5)6227749 ; +52(73)291749 62251 Cuernavaca, Morelos | MEXICO | FAX: +52(5)6227775 & +52(73)291775 ___________________________________EOF ____________________________________ From chemistry-request@server.ccl.net Thu Feb 10 20:50:53 2000 Received: from eros.iqm.unicamp.br (eros.iqm.unicamp.br [143.106.51.200]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA25553 for ; Thu, 10 Feb 2000 20:50:51 -0500 Received: (from hermes@localhost) by eros.iqm.unicamp.br (8.9.2/8.8.8) id WAA11056 for chemistry@ccl.net; Thu, 10 Feb 2000 22:43:23 -0200 (EDT) (envelope-from hermes) Date: Thu, 10 Feb 2000 22:43:22 -0200 From: Hermes Fernandes de Souza To: chemistry@ccl.net Subject: Values of density experimental for amorphous Message-ID: <20000210224322.A11015@eros.iqm.unicamp.br> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.5i Hi CCLers, I am looking for density experimental values for silicon and germanium amorphous. Can any one help me? Thanks, Hermes From chemistry-request@server.ccl.net Thu Feb 10 18:26:57 2000 Received: from Post-Office.UH.EDU (Post-Office.UH.EDU [129.7.1.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA24907 for ; Thu, 10 Feb 2000 18:26:57 -0500 Received: from POP.UH.EDU (POP.UH.EDU [129.7.1.28]) by Post-Office.UH.EDU (PMDF V5.2-32 #40812) with ESMTP id <0FPQ00CE4JCHKC@Post-Office.UH.EDU> for chemistry@ccl.net; Thu, 10 Feb 2000 16:19:29 -0600 (CST) Received: from uh.edu (kwlee@k9.BCHS.UH.EDU [129.7.40.218]) by POP.UH.EDU (PMDF V5.2-32 #40812) with ESMTP id <0FPQ00OBJJCBE9@POP.UH.EDU> for chemistry@ccl.net; Thu, 10 Feb 2000 16:19:27 -0600 (CST) Date: Thu, 10 Feb 2000 16:18:38 -0600 From: Keun Woo Lee Subject: Autodock3.0 gpf parameter problem. Sender: kwlee@UH.EDU To: chemistry@ccl.net Message-id: <38A3393D.C50D8F78@uh.edu> MIME-version: 1.0 X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.12-20 i686) Content-type: multipart/alternative; boundary="Boundary_(ID_Y8oY3+vejVPnglJoeTKDyg)" X-Accept-Language: en --Boundary_(ID_Y8oY3+vejVPnglJoeTKDyg) Content-type: text/plain; charset=EUC-KR Content-transfer-encoding: 7BIT Hello, I am currently using AUTODOCK3.0 but recently I found there are two parameters for GPF file (i.e. for making GRID map files) as the followings: Case 1. ---------------------------------------------- map protein.C.map #filename of grid map nbp_r_eps 4.00 0.0222750 12 6 #C-C lj nbp_r_eps 3.75 0.0230026 12 6 #C-N lj nbp_r_eps 3.60 0.0257202 12 6 #C-O lj nbp_r_eps 4.00 0.0257202 12 6 #C-S lj nbp_r_eps 3.00 0.0081378 12 6 #C-H lj nbp_r_eps 3.00 0.0081378 12 6 #C-H lj nbp_r_eps 3.00 0.0081378 12 6 #C-H lj sol_par 12.77 0.6844 constant 0.000 ----------------------------------------------- Case 2. ----------------------------------------------- map protein.C.map #atomic_affinity_map nbp_r_eps 4.00 0.1500 12 6 #C-C non-bond Rij & epsilonij nbp_r_eps 3.75 0.1549 12 6 #C-N non-bond Rij & epsilonij nbp_r_eps 3.60 0.1732 12 6 #C-O non-bond Rij & epsilonij nbp_r_eps 4.00 0.1732 12 6 #C-S non-bond Rij & epsilonij nbp_r_eps 3.00 0.0548 12 6 #C-H non-bond Rij & epsilonij nbp_r_eps 3.00 0.0548 12 6 #C-H non-bond Rij & epsilonij nbp_r_eps 3.00 0.0548 12 6 #C-H non-bond Rij & epsilonij --------------------------------------------- In the Autodock homepage in Schripps ( http://www.scripps.edu/pub/olson-web/doc/autodock/), the Case2 is listed in the parameter page. But in FAQ page, the Case 1 parameter is listed. In AUTODOCK3.0 manual, the Case2 parameter was used in the example xxx.gpf file in appendix. In the results of the calculation for both, the Docking energy of Case2 is lower than Case1 by about seven times. Which one is right ? Can you someone give me the answer or some clue about this ? Thank you in advance. Kunu ============================================== Keun Woo Lee, Ph.D. Postdoctoral Associate Department of Biology and Biochemistry University of Houston Houston, TX 77204-5513 Phone: (713) 743-8389, 8367 Fax: (713) 743-8351 Email: kwlee@uh.edu http://adrik.bchs.uh.edu/~kwlee ============================================== --Boundary_(ID_Y8oY3+vejVPnglJoeTKDyg) Content-type: text/html; charset=EUC-KR Content-transfer-encoding: 7BIT Hello,

I am currently using AUTODOCK3.0 but recently I found there are two parameters
for GPF file (i.e. for making GRID map files) as the followings:

<For example for Carbon atom>
Case 1.
----------------------------------------------
map  protein.C.map #filename of grid map
nbp_r_eps 4.00 0.0222750 12 6 #C-C lj
nbp_r_eps 3.75 0.0230026 12 6 #C-N lj
nbp_r_eps 3.60 0.0257202 12 6 #C-O lj
nbp_r_eps 4.00 0.0257202 12 6 #C-S lj
nbp_r_eps 3.00 0.0081378 12 6 #C-H lj
nbp_r_eps 3.00 0.0081378 12 6 #C-H lj
nbp_r_eps 3.00 0.0081378 12 6 #C-H lj
sol_par 12.77 0.6844
constant 0.000
-----------------------------------------------

Case 2.
-----------------------------------------------
map protein.C.map           #atomic_affinity_map
nbp_r_eps  4.00 0.1500  12   6  #C-C non-bond Rij & epsilonij
nbp_r_eps  3.75 0.1549  12   6  #C-N non-bond Rij & epsilonij
nbp_r_eps  3.60 0.1732  12   6  #C-O non-bond Rij & epsilonij
nbp_r_eps  4.00 0.1732  12   6  #C-S non-bond Rij & epsilonij
nbp_r_eps  3.00 0.0548  12   6  #C-H non-bond Rij & epsilonij
nbp_r_eps  3.00 0.0548  12   6  #C-H non-bond Rij & epsilonij
nbp_r_eps  3.00 0.0548  12   6  #C-H non-bond Rij & epsilonij
---------------------------------------------

In the Autodock homepage in Schripps (
http://www.scripps.edu/pub/olson-web/doc/autodock/), the Case2 is
listed in the parameter page. But in FAQ page, the Case 1 parameter
is listed. In AUTODOCK3.0 manual, the Case2 parameter was used
in the example xxx.gpf file in appendix.

In the results of the calculation for both,  the Docking energy of Case2 is
lower than Case1 by about seven times.

Which one is right ? Can you someone give me the answer or some clue
about this ?

Thank you in advance.

Kunu
  

 
==============================================
    Keun Woo Lee,  Ph.D.
    Postdoctoral Associate 
    Department of Biology and Biochemistry 
    University of Houston 
    Houston, TX 77204-5513 
    Phone: (713) 743-8389, 8367 
    Fax:   (713) 743-8351 
    Email:  kwlee@uh.edu 
    http://adrik.bchs.uh.edu/~kwlee
==============================================
  --Boundary_(ID_Y8oY3+vejVPnglJoeTKDyg)-- From chemistry-request@server.ccl.net Thu Feb 10 19:19:08 2000 Received: from harfang.CC.UMontreal.CA (harfang.CC.UMontreal.CA [132.204.2.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id TAA25162 for ; Thu, 10 Feb 2000 19:19:08 -0500 Received: from balzac.CERCA.UMontreal.CA (balzac.CERCA.UMontreal.CA [132.204.150.21]) by harfang.CC.UMontreal.CA (8.8.8/8.8.8) with ESMTP id SAA09043 for ; Thu, 10 Feb 2000 18:11:45 -0500 (EST) Received: from pellan.CERCA.UMontreal.CA (pellan.CERCA.UMontreal.CA [132.204.150.49]) by balzac.CERCA.UMontreal.CA (8.9.3/8.9.3) with ESMTP id SAA26906 for ; Thu, 10 Feb 2000 18:11:28 -0500 (EST) From: Suzanne Sirois Received: (from siroiss@localhost) by pellan.CERCA.UMontreal.CA (980427.SGI.8.8.8/8.8.8) id SAA29897 for chemistry@ccl.net; Thu, 10 Feb 2000 18:11:28 -0500 (EST) Message-Id: <200002102311.SAA29897@pellan.CERCA.UMontreal.CA> Subject: RE:Anybody agrees with me To: chemistry@ccl.net Date: Thu, 10 Feb 2000 18:11:27 -0500 (EST) X-Mailer: ELM [version 2.4ME+ PL66 (25)] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Although Arthur comments on Macromodel were personal, I do agree with the needs of standards. 1) Genomics and proteomics are fields that are developing at a very rapid speed. Soon we won`t not only use babel to convert file formats but we will also be in a Babel`s tower. In my opinion there is two life sciences area of applications that currently need standards: 1) GUI 2) Methods This sounds to me like classes in OOP. 1) Hence we can focus on developing standard classes for GUI that will inherit all the properties needed for a particular application. This will leave room to every developer to adapt its GUI to its own program. 2) About methods such as force fields, we can for example develop a class call force fields that will implements all the basic information that make up a FF. This will leave to the developers the opportunity to expand its method while inheriting basic components. 3) And so on. 4) Lets recall there is a language named CML that is currently under development for WEB application. How does it fit the needs for standards? Best regards to all Suzanne Sirois, Ph.D. Computational Chemist ChemInformaticien