From chemistry-request@server.ccl.net Fri Feb 11 03:37:42 2000 Received: from hydra.chem.rug.nl (hydra.chem.rug.nl [129.125.35.229]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA27221 for ; Fri, 11 Feb 2000 03:37:42 -0500 Received: from [129.125.7.13] (theochem1.chem.rug.nl [129.125.7.13]) by hydra.chem.rug.nl (AIX4.2/UCB 8.7/8.7) with ESMTP id IAA27088 for ; Fri, 11 Feb 2000 08:30:13 +0100 (MET) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" X-Sender: swart@hydra.chem.rug.nl Message-Id: In-Reply-To: <001701bf73c6$955de220$b91f84a5@yonsei.ac.kr> Date: Fri, 11 Feb 2000 08:34:02 +0100 To: CHEMISTRY@ccl.net From: Marcel Swart Subject: Re: CCL:Add hydrogen to the pdb file >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 not aware of any program that can do such a thing exactly, because the pH is not the only issues. It depends on the particular protein, whether some amino acids are actually protonated or not. However, I know that Gromacs is able to add hydrogens, and in my own experience they do a good job (also for the same protein with two different pH's): http://rugmd0.chem.rug.nl/~gmx The program you are looking for is pdb2gmx. Hope this helps, Marcel Swart. ============================================================== Marcel Swart E-mail : m.swart@chem.rug.nl ============================================================== From chemistry-request@server.ccl.net Fri Feb 11 04:24:14 2000 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA27680 for ; Fri, 11 Feb 2000 04:24:11 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Fri, 11 Feb 2000 09:17:55 +0100 Message-ID: <002301bf7468$65512220$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: References: <200002101731.LAA02436@hecuba.chem.ksu.edu> Subject: Re: CCL:Anybody agrees with me? Date: Fri, 11 Feb 2000 09:17:10 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 > 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. Agree! Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. L. Kossuth University, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 316666/2472 fax: (+36-52) 512914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm From chemistry-request@server.ccl.net Fri Feb 11 02:01:30 2000 Received: from smtp.csc.fi (pobox5.csc.fi [193.166.0.99]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA26913 for ; Fri, 11 Feb 2000 02:01:29 -0500 Received: from isosirri (isosirri.csc.fi [193.166.1.218]) by smtp.csc.fi (8.9.3/8.9.3/CSC) with SMTP id HAA15242; Fri, 11 Feb 2000 07:52:50 +0200 From: "Leif Laaksonen" To: "Ray Crawford" , "Angelo R. Rossi" Cc: "Renxiao Wang" , "Computational Chemistry List" Subject: RE: Anybody agrees with me? Date: Fri, 11 Feb 2000 07:55:21 +0200 Message-ID: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----=_NextPart_000_0000_01BF7465.5847E990" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) In-Reply-To: Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6700 This is a multi-part message in MIME format. ------=_NextPart_000_0000_01BF7465.5847E990 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Hi, I myself find this discussion quite interesting. However, I do not agree about all presented and then I'm a bit confused about some things but all in all I think it's good to talk about these matters >from time to time. After all we have to remember that we have come a long way along the standardization lines. Most graphics applications use OpenGL and Motif is specially used in the Unix field. Thinking about the situation some 15 years ago was a bit chaotic. So the libraries and tools "under the hood" have converged. This also makes the GUIs look very much alike, how they are setup and how they work is an other matter. Not so far in the past (a few monts) we had a discussion about XML/RDF on the CCL list. These tools will standardize again the data (knowledge) exchange between applications. Looking at the work the Computer-Human interface Usability group is doing at the close by Helsinki University of Technology I understand that my program(s) will always have an unusable GUI. This really takes time and money. Looking at things on a short time scale things might look chaotic but on a longer time scale I'm not so worried. This was my two Finn marks wort opinion as long as they are valid before the Euro comes... Regards, -leif laaksonen -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of Ray Crawford Sent: 10. helmikuuta 2000 19:58 To: Angelo R. Rossi Cc: Renxiao Wang; Computational Chemistry List Subject: CCL:Anybody agrees with me? 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 ------=_NextPart_000_0000_01BF7465.5847E990 Content-Type: text/x-vcard; name="Leif Laaksonen.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="Leif Laaksonen.vcf" BEGIN:VCARD VERSION:2.1 N:Laaksonen;Leif FN:Leif Laaksonen ORG:Center for Scientific Computing;FUNET TITLE:Network Information Services Manager NOTE:My personal Web page: http://www.csc.fi/~laaksone/ TEL;WORK;VOICE:+358 9 457 2378 TEL;CELL;VOICE:+358 +358400425203 TEL;WORK;FAX:+358 9 457 2302 ADR;WORK;ENCODING=QUOTED-PRINTABLE:;;Tekniikantie 15 a D=0D=0AP.O.Box 405;Espoo;;FIN-02101;Finland LABEL;WORK;ENCODING=QUOTED-PRINTABLE:Tekniikantie 15 a D=0D=0AP.O.Box 405=0D=0AEspoo FIN-02101=0D=0AFinland URL:http://laaksonen.csc.fi/ URL:http://www.csc.fi/ EMAIL;PREF;INTERNET:Leif.Laaksonen@csc.fi EMAIL;INTERNET:Leif.Laaksone@csc.fi REV:19991226T172416Z END:VCARD ------=_NextPart_000_0000_01BF7465.5847E990-- From chemistry-request@server.ccl.net Fri Feb 11 05:33:38 2000 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA28166 for ; Fri, 11 Feb 2000 05:33:36 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Fri, 11 Feb 2000 10:26:57 +0100 Message-ID: <003d01bf7472$06d3c9a0$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: References: Subject: CCL:Anybody agrees with me? Date: Fri, 11 Feb 2000 10:26:05 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 I think that *some* unofficial standardisation of the GUI could be beneficial, for example: manipulation of a structure with the mouse: left-click + drag: x and y rotation of the structure, shift left-click + drag : zoom up/down, shift right-click + drag : z rotation, ctrl right-click + drag: x y translate, etc However, it must be taken into consideration that a scientific software is not the same category as text editors like Word or WordPerfect etc., and is not intended for the use of secretaries and typists. Consider for example the programs, which offer an interface to MOPAC or has a built-in MOPAC module. MOPAC has several dozens of keywords and parameters and options, the number of combinations is immense. These programs usually offer a few general options for an average geometry optimalization and the calculation of a few properties. But MOPAC knows much more, and if one wants something different, the use of keywords is inevitable. Many people hates this type of command line input and wants "some user-friendly" method, but how could it be done? If a MOPAC interface would appear with two hundreds of buttons and drop-down menus and input boxes on the screen, it would also be regarded very unfriendly. As somebody wrote, "...the more an interface can do, the more difficult it is to make it user friendly". I think that the planning and realization of a good interface is usually more complicated and time-consuming as the program itself. On the other hand, the most contraversary thing is that the interface should do many-many things (therefore it tends to be complicated), but most people hate reading manuals and online helps. Therefore many features, options and bells-and-whistles of the program remain unknown to them, thus they start with another program and so on. An interface is not complicated if one takes time to get aquinted with it. Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. L. Kossuth University, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 316666/2472 fax: (+36-52) 512914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm From chemistry-request@server.ccl.net Fri Feb 11 06:04:57 2000 Received: from gensig.nibsc.ac.uk (gensig.nibsc.ac.uk [193.62.43.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA28411 for ; Fri, 11 Feb 2000 06:04:56 -0500 Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by gensig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA74388; Fri, 11 Feb 2000 09:54:35 GMT Message-ID: <38A3DCF6.A20D5B1@nibsc.ac.uk> Date: Fri, 11 Feb 2000 09:57:10 +0000 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: Marcel Swart , chemistry@server.ccl.net Subject: Re: CCL:Add hydrogen to the pdb file References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Marcel For a free code that adds hydrogens to a PDB file try the weblab viewer Lite from MSI. It does not take pH as a parameter. http://www.msi.com Best Wishes Mark F Marcel Swart wrote: > >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 not aware of any program that can do such a thing exactly, because the > pH is not the only issues. It depends on the particular protein, whether > some amino acids are actually protonated or not. > > However, I know that Gromacs is able to add hydrogens, and in my own > experience they do a good job (also for the same protein with two different > pH's): > > http://rugmd0.chem.rug.nl/~gmx > > The program you are looking for is pdb2gmx. > > Hope this helps, > > Marcel Swart. > ============================================================== > Marcel Swart > > E-mail : m.swart@chem.rug.nl > ============================================================== > > -= 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 -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@server.ccl.net Fri Feb 11 07:37:24 2000 Received: from admin.cnrs-orleans.fr (admin.cnrs-orleans.fr [163.9.1.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA29680 for ; Fri, 11 Feb 2000 07:37:20 -0500 From: hinsen@cnrs-orleans.fr Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id MAA05308 ; Fri, 11 Feb 2000 12:29:45 +0100 (MET) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id MAA03330; Fri, 11 Feb 2000 12:30:00 +0100 Date: Fri, 11 Feb 2000 12:30:00 +0100 Message-Id: <200002111130.MAA03330@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f To: renxiao@chem.ucla.edu CC: chemistry@ccl.net In-reply-to: (message from Renxiao Wang on Wed, 9 Feb 2000 15:43:05 -0800 (PST)) Subject: Re: CCL:Anybody agrees with me? References: > Maybe you will argue that every software has its own advantages and > disadvantages. I agree. But this should not be the reason why those > softwares are so different in interface! I have experience in using quite Sure, standardization had advantages. But standardizing in some evolving field can also limit improvements significantly. I don't think that interactive modelling software already has already reached the point where everyone agrees how things should work and disagreement is only over minor details. So my answer is: not yet. On the other hand, something that should be more standardized is file formats. If data could be interchanged freely, people could use different programs together more effectively. As a first step, all producers of scientific software, academic and commercial, should document the file formats they use. And then they should get together and agree on standards. And I mean well-defined and usable standards, to prevent chaotic developments as we have seen with the PDB format. -- ------------------------------------------------------------------------------- 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@server.ccl.net Fri Feb 11 07:38:42 2000 Received: from hqix.hydroqual.com ([207.198.247.3]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA29691 for ; Fri, 11 Feb 2000 07:38:41 -0500 Received: by www.comcarto.com with Internet Mail Service (5.5.2448.0) id <1FQ4601S>; Fri, 11 Feb 2000 06:20:17 -0500 Message-ID: <21E773485C55D21184F900C0F01502C947470A@www.comcarto.com> From: dominic ditoro To: "'chemistry@ccl.net'" Subject: Gaussian, Linda, and PC clusters Date: Fri, 11 Feb 2000 06:20:16 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain; charset="iso-8859-1" We have ~10k$ to spend in the near future at which point it evaporates... We are considering purchasing a cluster of fast PC's, say 4 machines initially (700 Mhz or so, 256Mb, 8 GB), to run Gaussian using linux and Linda. Has anyone had any experience with this sort of configuration. We guess that it will be roughly 5-7 times faster than our present single 400 Mhz machines. We don't have the resources to endlessly baby sit the cluster. So the ease of use is as important as performance. Our vision is that compiled code will arrive from Gaussian, we install the appropriate linux os, load the code and start computing. Is this living in dreamland? Finally, any experience with running highlevel methods, e.g. G2, on a cluster? Either public or private responses are welcome. I will summerize. Dominic M. Di Toro Professor Environmental Engineering Manhattan College, Riverdale NY dditoro@hydroqual.com From chemistry-request@server.ccl.net Fri Feb 11 07:45:09 2000 Received: from admin.cnrs-orleans.fr (admin.cnrs-orleans.fr [163.9.1.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA29780 for ; Fri, 11 Feb 2000 07:45:07 -0500 From: hinsen@cnrs-orleans.fr Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id MAA05621 ; Fri, 11 Feb 2000 12:37:33 +0100 (MET) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id MAA03334; Fri, 11 Feb 2000 12:37:45 +0100 Date: Fri, 11 Feb 2000 12:37:45 +0100 Message-Id: <200002111137.MAA03334@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f To: siroiss@CERCA.UMontreal.CA CC: chemistry@ccl.net In-reply-to: <200002102311.SAA29897@pellan.CERCA.UMontreal.CA> (message from Suzanne Sirois on Thu, 10 Feb 2000 18:11:27 -0500 (EST)) Subject: Re: CCL:RE:Anybody agrees with me References: <200002102311.SAA29897@pellan.CERCA.UMontreal.CA> > 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. Well, yes, but it's not that easy... > 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. This has been going on for quite a while now. There are dozens of GUI libraries, each of which claims to be standard, portable, etc. I don't mean to say that GUI libraries are useless. They make using GUIs a lot easier. But it seems that standardization is still in the remote future. > 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. This is exactly the approach I have been following with my OpenSource simulation library, the Molecular Modeling Toolkit (http://starship.python.net/crew/hinsen/MMTK/). In my experience, it greatly facilitates the development and implementation of new methods. Nevertheless, I don't expect this (or any similar) library to become "standard" soon; the approach is too new to be sure that a given design will be good enough for the forseeable future. > 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? It attempts to provide standard data formats for certain applications, which is definitely A Good Thing. I am not happy with CML in particular, because it leaves many details open to interpretation. But I do expect that XML-based file formats will help in creating standard file formats. -- ------------------------------------------------------------------------------- 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@server.ccl.net Fri Feb 11 05:36:46 2000 Received: from yogi.pc1.uni-duesseldorf.de (root@yogi.pc1.uni-duesseldorf.de [134.99.152.44]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA28219 for ; Fri, 11 Feb 2000 05:36:45 -0500 Received: (from jochen@localhost) by yogi.pc1.uni-duesseldorf.de (8.9.3/8.9.3) id KAA00655; Fri, 11 Feb 2000 10:28:49 +0100 From: "Jochen Küpper" MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Message-ID: <14499.54864.128053.973672@yogi.pc1.uni-duesseldorf.de> Date: Fri, 11 Feb 2000 10:28:48 +0100 (CET) To: Ramon Garduno Cc: chemistry@ccl.net Subject: CCL:POSTSCRIPT VIEWER...HELP!!! In-Reply-To: <200002110150.RAA04488@ce.fis.unam.mx> References: <200002110150.RAA04488@ce.fis.unam.mx> X-Mailer: VM 6.71 under 21.1 (patch 4) "Arches" XEmacs Lucid Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id FAA28220 Ramon Garduno writes: > CCL topic, but I have tried to install GHOSTVIEW in my SGI Octane, and > I can do it right. Fine :-) > 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 Well, that's not ghostview, but gv, I guess :-) Why don't you use gs itself, plain old ghostview, mgv (Motif gv), ... ? More over there is a SGI postscript viewer with IRIX, IIRC. It might be called psview (Sorry, I mislike SGI's :-) If you cannot install Xaw3d yourself, I would advice you to use one of the ps-viewers delivered by SGI, either within IRIX or on the add. software CDs. Jochen -- Heinrich-Heine-Universität Institut für Physikalische Chemie I Jochen Küpper Universitätsstr. 1, Geb. 26.43.02.29 40225 Düsseldorf, Germany phone ++49-211-8113681, fax ++49-211-8115195 http://www.jochen-kuepper.de From chemistry-request@server.ccl.net Fri Feb 11 05:46:12 2000 Received: from gensig.nibsc.ac.uk (gensig.nibsc.ac.uk [193.62.43.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA28305 for ; Fri, 11 Feb 2000 05:46:10 -0500 Received: from nibsc.ac.uk (dlinmf.nibsc.ac.uk [193.62.42.144]) by gensig.nibsc.ac.uk (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id JAA61060 for ; Fri, 11 Feb 2000 09:35:50 GMT Message-ID: <38A3D892.5928E46@nibsc.ac.uk> Date: Fri, 11 Feb 2000 09:38:26 +0000 From: Mark Forster Organization: NIBSC X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: RE:Anybody agrees with me Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Comp. Chemists This raises a very important point about user interface design. There is, IMHO, a trade off to be made between simplicity (few features, easy to to understand, aimed at the novice user) and flexibility (lots of features, as many options as possible, aimed at the expert user). If you want to name names, then I would agree that the insightII and Quanta, for example, are quite complicated interfaces, but they are very comprehensive codes that cover a wide range of application areas. The idea that a standard GUI can be developed is neither feasible nor desirable. Different codes are aimed at different markets and categories of users and this can often determine how their GUI is designed. Even under a single opearating system and GUI paradigm, say Windows 9x, GUI design can vary widely. The X windows system will not lead to any degree of standardisation. There are many different window managers allowed even for one version of Unix. Hence a more basic level of standardisation is needed for Unix before unification of GUIs can even be considered. This is not to say that a comprehensive software tool cannot have an intuitive GUI, but achieving that balance needs careful design, and the designer must be someone who understands the process of GUI design as well as the area of science encapsulated by the code. Horses for courses. Best Wishes Mark F -- Dr Mark J Forster Ph.D. Principal Scientist Informatics Laboratory National Institute for Biological Standards and Control Blanche Lane, South Mimms, Hertfordshire EN6 3QG, United Kingdom. Tel +44 (0)1707 654753 FAX +44 (0)1707 646730 E-mail mforster@nibsc.ac.uk From chemistry-request@server.ccl.net Fri Feb 11 09:07:57 2000 Received: from mserv.rug.ac.be (mserv.rug.ac.be [157.193.40.37]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA30267 for ; Fri, 11 Feb 2000 09:07:56 -0500 Received: from allserv.rug.ac.be (allserv.rug.ac.be [157.193.40.42]) by mserv.rug.ac.be (8.9.3/8.9.3) with ESMTP id OAA08004 for ; Fri, 11 Feb 2000 14:00:22 +0100 (MET) Received: from houston (houston.rug.ac.be [157.193.89.160]) by allserv.rug.ac.be (8.9.3/8.9.3) with SMTP id NAA28379 for ; Fri, 11 Feb 2000 13:59:46 +0100 (MET) Received: by localhost with Microsoft MAPI; Fri, 11 Feb 2000 14:00:36 +0100 Message-ID: <01BF7498.5EBF7580.jeanluc.verschelde@rug.ac.be> From: Verschelde Jean-Luc To: "'CCL'" Subject: amber5 and mpich Date: Fri, 11 Feb 2000 13:48:59 +0100 X-Mailer: Microsoft Internet E-mail/MAPI - 8.0.0.4211 MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear all, I ssj I have still a lot of trouble running sander on a cluster of dec alpha's with os redhat 5.2 and MPICH. When sander calls the balance routine it stops and gives following messages: p1_5991: p4_error: interrupt SIGSEGV: 11 rm_l_1_5992: p4_error: interrupt SIGINT: 2 p0_1383: p4_error: interrupt SIGSEGV: 11 bm_list_1384: p4_error: interrupt SIGINT: 2 rm_l_3_4989: p4_error: interrupt SIGINT: 2 rm_l_2_5417: p4_error: interrupt SIGINT: 2 [jeanluc@genesis actin]$ p2_5416: p4_error: interrupt SIGINT: 2 p3_4988: p4_error: interrupt SIGINT: 2 When I put ilbnob = 1 in the input file, I receive this: rm_l_1_6003: p4_error: net_recv read: probable EOF on socket: 1 Illegal instruction rm_l_2_5430: p4_error: net_recv read: probable EOF on socket: 1 rm_l_3_5000: p4_error: net_recv read: probable EOF on socket: 1 Illegal instruction Illegal instruction bm_list_1520: p4_error: net_recv read: probable EOF on socket: 1 Any help is appreciated, Verschelde Jean-Luc From chemistry-request@server.ccl.net Fri Feb 11 10:36:38 2000 Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA30823 for ; Fri, 11 Feb 2000 10:35:36 -0500 Received: from anti07 (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP for ; Fri, 11 Feb 2000 15:28:56 +0100 Message-ID: <000d01bf749c$3419f5e0$3b8506c1@chem.klte.hu> From: "Tamas E. Gunda" To: References: <001701bf73c6$955de220$b91f84a5@yonsei.ac.kr> Subject: Re: CCL:Add hydrogen to the pdb file Date: Fri, 11 Feb 2000 15:28:01 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2615.200 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2615.200 Original message: >Subject: CCL:Add hydrogen to the pdb file > 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. > Mol2Mol can do that, although not in pH-dependent mode (and it is not freeware, look http://www.compuchem.com) Dr Tamas E. Gunda Research Group for Antibiotics of the Hungarian Acad. Sci. L. Kossuth University, POBox 36 H-4010 Debrecen, Hungary tel.: (+36-52) 316666/2472 fax: (+36-52) 512914 e-mail: tamasgunda@tigris.klte.hu home-page: www.klte.hu/~gundat/gunda.htm From chemistry-request@server.ccl.net Fri Feb 11 10:38:15 2000 Received: from ns02.sbphrd.com (firewall-user@ns02.sbphrd.com [208.198.64.2]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA30831 for ; Fri, 11 Feb 2000 10:38:14 -0500 Received: by ns02.sbphrd.com; id JAA24216; Fri, 11 Feb 2000 09:30:41 -0500 Received: from unknown(139.136.64.5) by ns02.sbphrd.com via smap (V5.0) id xma024196; Fri, 11 Feb 00 09:30:27 -0500 Received: from hbu037.ha.uk.sbphrd.com (hbu037.ha.uk.sbphrd.com [139.136.216.37]) by phinet.sbphrd.com (8.9.1b+Sun/8.9.1) with ESMTP id JAA09849 for ; Fri, 11 Feb 2000 09:30:37 -0500 (EST) Received: from hgu094.ha.uk.sbphrd.com (hgu094.ha.uk.sbphrd.com [139.136.157.94]) by hbu037.ha.uk.sbphrd.com (8.8.8/8.8.8/sbphrd/mh/19971204) with ESMTP id OAA26937 for ; Fri, 11 Feb 2000 14:30:25 GMT Received: from localhost (jenninaj@localhost) by hgu094.ha.uk.sbphrd.com (8.8.8/8.8.8) with ESMTP id OAA115254 for ; Fri, 11 Feb 2000 14:30:25 GMT X-Authentication-Warning: hgu094.ha.uk.sbphrd.com: jenninaj owned process doing -bs Date: Fri, 11 Feb 2000 14:30:25 +0000 From: Andy Jennings X-Sender: jenninaj@hgu094.ha.uk.sbphrd.com To: Comp-Chem-List Subject: Ongoing debate about standardisation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all I don't know about the debate re. GUIs as I personally believe that every persons view of what is 'right' is too subjective. What really bugs me is the plethora of file formats currently in use and the difficulties related to converting one into the other. Babel is very good but it is not perfect and some interconversions between formats can lead to _very_ strange results indeed. I understand why there have to be a certain number of formats (eg due to the atom-typing carried out for different force-fields) but I think a bit of rationalisation wouldn't go amiss. With more and more of us working with not just ones or tens of compounds but hundreds and even thousands, the idea of tweaking each structure manually is not just unattractive but in many cases impossible. The only analogy I can make over the current debate is related to automobiles: everyone has their own preference for style, size and colour but they all use just one of a very few choices of fuel. Flame-shields on!!!! Andy ================================================================= Andy Jennings SmithKline Beecham Pharmaceuticals "Quantum Mechanics: The dreams stuff is made of" From chemistry-request@server.ccl.net Fri Feb 11 10:58:32 2000 Received: from nmrc.ucc.ie (nmrc.ucc.ie [143.239.64.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA30943 for ; Fri, 11 Feb 2000 10:58:26 -0500 Received: from mailhost.nmrc.ucc.ie (gateway.nmrc.ucc.ie [10.1.64.2]) by nmrc.ucc.ie (Postfix) with ESMTP id A69BB4F8C for ; Fri, 11 Feb 2000 14:48:56 +0000 (GMT) Received: by mailhost.nmrc.ucc.ie (Postfix, from userid 1) id 16D26EED8; Fri, 11 Feb 2000 14:49:30 +0000 (GMT) Date: Fri, 11 Feb 2000 15:00:37 +0000 From: Michael Nolan To: ccl Subject: [jochen@uni-duesseldorf.de: CCL:POSTSCRIPT VIEWER...HELP!!!] Message-ID: <20000211150037.F3191@rennes.nmrc.ucc.ie> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i Netter's, just to Jochen's mail: >More over there is a SGI postscript viewer with IRIX, IIRC. >It might be called psview (Sorry, I mislike SGI's :-) > >If you cannot install Xaw3d yourself, I would advice you to use one of >the ps-viewers delivered by SGI, either within IRIX or on the >add. software CDs. On our SGI O_2 we have a ps viewer pre-installed called showps. It's from adobe systems. slainte mick -- ************************************************************************** Mr. Michael Nolan BSc. MEngSc. "What is a man that an electron Computational Modelling Group, NMRC is mindful of him?" Lee Maltings, Prospect Row, Cork, IRELAND mail: mnolan@nmrc.ucc.ie; http://nmrc.ucc.ie Tel: + 353 21 904113; Fax: +353 21 270271 *************************************************************************** From chemistry-request@server.ccl.net Fri Feb 11 11:31:24 2000 Received: from mail.sun.ac.za (mail.sun.ac.za [146.232.128.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA31283 for ; Fri, 11 Feb 2000 11:31:18 -0500 Received: from land.sun.ac.za ([146.232.216.2]) by mail.sun.ac.za with esmtp (Exim 2.10 #1) id 12JHuz-0004pM-01 for chemistry@ccl.net; Fri, 11 Feb 2000 17:23:37 +0200 Received: from SUN_LAND/SpoolDir by land.sun.ac.za (Mercury 1.44); 11 Feb 00 17:23:36 +0200 Received: from SpoolDir by SUN_LAND (Mercury 1.44); 11 Feb 00 17:23:16 +0200 Received: from maties (146.232.209.204) by land.sun.ac.za (Mercury 1.44); 11 Feb 00 17:23:08 +0200 Reply-To: From: "Jan Dillen" To: Subject: Anybody agrees with me? Date: Fri, 11 Feb 2000 17:23:07 +0200 Message-ID: <000801bf74a3$e62c08c0$ccd1e892@maties.sun.ac.za> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook 8.5, Build 4.71.2173.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Importance: Normal > I just cannot help wondering why the guys who > develop these molecular modeling softwares > have not met together and defined a "standard". I remember a time when some programs required a stack of 70 punch cards whereas others required 120 of them. Is is a pity people did not agree about a standard in those days. IMHO, "the guys who develop these molecular modeling softwares", are very hard working scientists whose prime concern is to get something useful out of the codes there develop, educate students, promote the science they embrace, and give their work away for free in the form of "simpler programs" to colleagues, co-workers, and yes, scientific competitors. We do have a standard in molecular modeling. Actually we have several. Three of them are "reading the manual", "cursing to the manual", and "re-writing the manual". Me, "tired of learning" ? No way!. Jan Dillen (A guy who develops molecular modeling software) From chemistry-request@server.ccl.net Fri Feb 11 11:15:07 2000 Received: from motgate2.mot.com (motgate2.mot.com [136.182.1.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA31062 for ; Fri, 11 Feb 2000 11:15:07 -0500 Received: [from pobox.mot.com (pobox.mot.com [129.188.137.100]) by motgate2.mot.com (VWALL-IN-motgate2 2.0) with ESMTP id IAA00612 for ; Fri, 11 Feb 2000 08:07:30 -0700 (MST)] Received: [from msgphx4.sps.mot.com (msgphx4.sps.mot.com [216.11.52.4]) by pobox.mot.com (MOT-pobox 2.0) with ESMTP id IAA05357 for ; Fri, 11 Feb 2000 08:07:29 -0700 (MST)] Received: from email.mot.com ([223.189.20.185]) by msgphx4.sps.mot.com (Netscape Messaging Server 3.61) with ESMTP id AAA99B; Fri, 11 Feb 2000 08:07:27 -0700 Sender: korkin@pobox.mot.com Message-ID: <38A424A6.D32D55BD@email.mot.com> Date: Fri, 11 Feb 2000 07:03:02 -0800 From: "Anatoli Korkin (r40757)" Organization: Motorola Semiconductor Products Sector X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: "Tamas E. Gunda" , CCL Subject: Re: CCL:Anybody agrees with me? References: <200002101731.LAA02436@hecuba.chem.ksu.edu> <002301bf7468$65512220$3b8506c1@chem.klte.hu> Content-Type: multipart/alternative; boundary="------------595DCC4E18905F84EB2E7B91" X-Motorola-Sent-Wireless: 1 --------------595DCC4E18905F84EB2E7B91 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Guys, Do not send such messages on CCL. Respect other people's time. I try to be loyal to CCL and Jan is my good friend, but I am getting sick sometimes just clicking on "delete" button mornings, when a few people get excited about something. My suggestion is simple. Create short term mailing groups on the topic, exhost yourself and send a summary to the rest of the world. If you want to learn how to do that I can help. Thanks a bunch, Anatoli "Tamas E. Gunda" wrote: > > 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. > > Agree! > > Dr Tamas E. Gunda > Research Group for Antibiotics of the Hungarian Acad. Sci. > L. Kossuth University, POBox 36 > H-4010 Debrecen, Hungary > tel.: (+36-52) 316666/2472 > fax: (+36-52) 512914 > e-mail: tamasgunda@tigris.klte.hu > home-page: www.klte.hu/~gundat/gunda.htm > > -= 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 -- ****************************************************************** Anatoli A. Korkin, Ph.D Advanced Systems Research Lab Computational Chemist Semiconductor Products Sector Motorola Inc., MD M360 Tel: (480) 655-3171 2200 W. Broadway Road Fax: (480) 655-5013 Mesa AZ 85202 E.mail: r40757@email.mot.com ******************************************************************* --------------595DCC4E18905F84EB2E7B91 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Guys,

Do not send such messages on CCL. Respect other people's time. I try to be loyal to CCL
and Jan is my good friend, but I am getting sick sometimes just clicking on "delete"
button mornings, when a few people get excited about something.

My suggestion is simple. Create short term mailing groups on the topic, exhost yourself
and send a summary to the rest of the world. If you want to learn how to do that I can help.

Thanks a bunch,

Anatoli

"Tamas E. Gunda" wrote:

> 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.

Agree!

Dr Tamas E. Gunda
Research Group for Antibiotics of the Hungarian Acad. Sci.
L. Kossuth University, POBox 36
H-4010 Debrecen, Hungary
tel.: (+36-52) 316666/2472
fax: (+36-52) 512914
e-mail: tamasgunda@tigris.klte.hu
home-page: www.klte.hu/~gundat/gunda.htm

-= 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

-- 
******************************************************************

Anatoli A. Korkin, Ph.D         Advanced Systems Research Lab
Computational Chemist           Semiconductor Products Sector

Motorola Inc., MD M360          Tel:    (480) 655-3171
2200 W. Broadway Road           Fax:    (480) 655-5013
Mesa AZ 85202                   E.mail: r40757@email.mot.com
                                        
*******************************************************************
  --------------595DCC4E18905F84EB2E7B91-- From chemistry-request@server.ccl.net Fri Feb 11 10:53:26 2000 Received: from kodakr.kodak.com (kodakr.kodak.com [192.232.119.69]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA30902 for ; Fri, 11 Feb 2000 10:53:26 -0500 Received: from mozart.rl.kodak.com (mozart.rl.kodak.com [150.220.76.27]) by kodakr.kodak.com (8.9.1/8.9.1) with ESMTP id JAA10666 for <@mail.rl.kodak.com:CHEMISTRY@ccl.net>; Fri, 11 Feb 2000 09:45:52 -0500 (EST) Received: from mozart.rl.kodak.com (berlioz [150.220.89.22]) by mozart.rl.kodak.com (980427.SGI.8.8.8/950213.SGI.AUTOCF) via ESMTP id JAA70160 for ; Fri, 11 Feb 2000 09:49:30 -0500 (EST) Sender: david.giesen@kodak.com Message-ID: <38A41B30.B8F4994C@mozart.rl.kodak.com> Date: Fri, 11 Feb 2000 09:22:40 -0500 From: David Giesen Organization: Eastman-Kodak X-Mailer: Mozilla 4.05C-SGI [en] (X11; U; IRIX64 6.5 IP25) MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Standardizing Interfaces Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Careful, there may be some grouchy rumblings ahead, but I promise not to mention any programs by name.. :) Who would have thought that simply asking for more user-friendly interfaces would have raised such animosity??? When you get right down to it, a plea to standardize interfaces is about being user-friendly. If I know how to use 15 different molecular drawing GUI's, but I can't easily figure out how to delete an atom or measure a bond length in a new program, than I don't care how cute the buttons are, it isn't user friendly. It would be ridiculous to suggest that every aspect of a comp chem program can be standardized. Lots of people smarter than I have hammered that point home over the last few days. But just because one program can view biological molecules using helices and sheets, does that mean that the button for deleting a bond has to look like a paper towel dispenser, while the program for building 20 atom derivatives of benzene must use a button for the same purpose that looks like a skyscraper being attacked by giant eagles? Obviously, I've broken into hyperbole to make a point (and now just gotten redundant), but other software industries have caught on to standard interfaces, why must we be so haughty as to suggest that 'we do too many different things' to care about the user? The spray paint icon in the latest version of a $$$ package like Adobe Photoshop purchased in 2000 for a PC looks virtually identical to the spray paint icon in the shareware Mac program I was using in 1988. When I see an icon of a disk, I know it means to save my document, whether I'm using a Word processor, spread sheet, molecular editor (etc etc etc), the year is 1984 or 2000, and the platform is Mac, PC, SGI or Linux. So please don't tell me that comp chem software is too new, or too varied, or that not standardizing is fighting the good fight against software tyranny. There is a basic functionality that most comp chem interfaces share. They could be very easily standardized. Of course, what the standard is and who decides that would be a ten year debate, but that doesn't mean it can't be done, only that it hasn't. Wow - I must have skipped breakfast today to get this grumpy! Dave -- Dr. David J. Giesen Eastman Kodak Company david.giesen@kodak.com 2/83/RL MC 02216 (ph) 1-716-58(8-0480) Rochester, NY 14650 (fax)1-716-722-2327 From chemistry-request@server.ccl.net Fri Feb 11 11:57:14 2000 Received: from dedalus.lcc.ufmg.br (dedalus.lcc.ufmg.br [150.164.65.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA31732 for ; Fri, 11 Feb 2000 11:57:12 -0500 Received: from localhost (rkrocha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id NAA06928 for ; Fri, 11 Feb 2000 13:49:34 -0200 Date: Fri, 11 Feb 2000 13:49:34 -0200 (BDB) From: ramon kleber da rocha Reply-To: ramon kleber da rocha To: Computational Chemistry Mailing List Subject: Summary: Molecular Modeling Exercises Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody Some times ago I posted a question about Molecular Modeling Exercises. Well, here is a summary of the replies I got. I'd like to thanks to Dr. Jeffrey Madura, Dr. Ray Fort Jr., Dr. Frank Jensen, Dr. Brian Williams and Dr. Carlos Frederico de Souza Castro for their replies. Summary: Two books were suggested: Molecular Mechanics acrooss Chemistry. Anthony Rappe and Carla Casewit ISBN:0-935702-77-6. Amazon price: $58,00. The Molecular Modeling Workbook for Organic Chemistry. Warren Hehre, Alan Shusterman and Janet Nelson. ISBN 1-890-661-06-6. One can find that book at: http://www.wavefun.com/books/books.html Three web sites were suggested: http://pollux.chem.umn.edu/~cramer/ http://bogense.chem.ou.dk/~icc/ http://www.chem.ucsb.edu/MolecularModeling/CaseStudyAch.html Best regards. ________________________________________________________________________________ Ramon Kleber da Rocha, MSc. VOICE +55-31-499-5765 e-mail rkrocha@dedalus.lcc.ufmg.br FAX +55-31-499-5700 Laboratorio de QSAR e Modelagem Molecular Nucleo de Estudos em Quimica Medicinal - NEQUIM - http://www.qui.ufmg.br/~nequim Departamento de Quimica - Instituto de Ciencias Exatas Universidade Federal de Minas Gerais Av. Presidente Antonio Carlos, 6627 Campus Pampulha CEP 31-270-901 - Belo Horizonte - Minas Gerais - Brasil --- The World is my Fatherland, Science is my Religion. Christiaan Huygens 1629-1695 ________________________________________________________________________________ From chemistry-request@server.ccl.net Fri Feb 11 13:24:03 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA32671 for ; Fri, 11 Feb 2000 13:24:03 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id MAA04328; Fri, 11 Feb 2000 12:16:25 -0500 (EST) Date: Fri, 11 Feb 2000 12:16:25 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski Subject: Re: CCL: From Your Coordinator: Anybody agrees with me? In-Reply-To: <000801bf74a3$e62c08c0$ccd1e892@maties.sun.ac.za> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear, Since we have an explosive discussion on the CCL, I need to say a word. Cool down... It is not the first time... 1) Some tell me that I should stop some voices from appearing on the list. Sorry to say, but I do not moderate the list, i.e., I am not reviewing messages which come to the list. If my software finds something which is suspicious, it stops it. I do not... As long as it is remotely about chemistry it CAN go to the list. AT THE SAME TIME, PLEASE!!! PLEASE!!! read the rules: http://www.ccl.net/chemistry/aboutccl/rules/ Why I do not censor the list? Because I would be liable, and would loose my "internet operator" status (a printing shop), and became an editor or a publisher, i.e., a person responsible for what is printed. Needless to say, at this moment I cannot afford to hire a few lawyers specializing in patent, defamation, copyright, etc., law which will review the stuff which is being posted. Sorry to say, but the battle for freedom of speech in the media is lost, at least in the US. It the lawyers den, and it is for big guys only. Small guys like me (or the "Village Inquirer" and likes) cannot stay in publishing business. 2) As to the standardization issue, I think that it would be much better for the discussion itself if it was less heated and had more practical suggestions. I do not think we will be able to standardize interfaces and GUIs easily. The problem is that the mouse on a Mac has one button, and on the SGI, it has 3 (with PC in the middle...). But of course, we can go a long way in having standard convention in visualization. And in fact we have, but you have to admit that this is the area of active development and research. In my opinion we could do a much faster progress in representing data uniformly, rather than on the GUI side. The issue of passing data between different packages from different vendors/authors/groups is really a pain, since more and more, we have to use methods in tandem. I am a great proponent of XML. PLEASE VISIT the: http://www.xml-cml.org/ PLEASE DO NOT FLAME ME FOR THIS. I am not talking about junking legacy formats!!! There is so much investment in them that it would be a tragedy if this happened overnight. I am asking developers to consider producing the both XML output and traditional output. It is only additional write statements. No big deal. The big deal is to agree what tags to use and what is the DTD. But even well formed XML will do. I believe that in the past, market forces were making managers believe that proprietary format is good for business and helps to have "loyal customers" (read: trapped customers). But it seems that at least some chemistry software developers realized quickly (and painfully) that: a) customers want interoperability, b) customers ain't stupid, and even managers who hold the purse do not believe the stories about solving science problems by clicking buttons. c) if you do not publish the input/output file formats, the people will tell you to go elsewhere. Yet still we develop thousands of filters, converters, and edit files so something else "can eat it". What a waste... Again... with the new XML paradigm, there is a chance. Everything is ASCII, free format, easily parsable, with ton of free and commercial parsers which can be plugged in (and BTW, everybody in this business wrote his 10 line long fast & dirty perl XML parser, including me). Please visit http://www.xml-cml.org/ (Yes, I have nothing to do with them). Chemists were first in this business, and we should continue to be there. I would strongly encourage software vendors and commercial users to support this initiative. Do you really want those physicists to do it again to us {:-)}... (do not ask me what... I am just teasing you guys...). Jan Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Fri Feb 11 15:29:59 2000 Received: from pollux.chem.umn.edu (pollux.chem.umn.edu [128.101.156.56]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA01077 for ; Fri, 11 Feb 2000 15:29:59 -0500 Received: (from cramer@localhost) by pollux.chem.umn.edu (8.9.3/8.9.3) id NAA21321 for chemistry@ccl.net; Fri, 11 Feb 2000 13:22:23 -0600 (CST) From: Christopher Cramer Message-Id: <200002111922.NAA21321@pollux.chem.umn.edu> Subject: CCL:Summary: Molecular Modeling Exercises (fwd) To: chemistry@ccl.net Date: Fri, 11 Feb 2000 13:22:23 -0600 (CST) X-Mailer: ELM [version 2.5 PL2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Re: > > Some times ago I posted a question about Molecular Modeling > Exercises. > (snip) > > Three web sites were suggested: > > http://pollux.chem.umn.edu/~cramer/ > (snip) While I'm flattered to have my personal webpage listed, I suspect the intent was to point you to my site for Chemistry 8021 (formerly called 8003) which has about six years worth of problem sets and answers for a graduate Computational Chemistry Class. While that site CAN be accessed >from my home page, it is more easily reached directly at http://pollux.chem.umn.edu/~kormos/8021/ Regards, Chris -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 -------------------------- Phone: (612) 624-0859 || FAX: (612) 626-2006 cramer@pollux.chem.umn.edu http://pollux.chem.umn.edu/~cramer From chemistry-request@server.ccl.net Fri Feb 11 14:54:00 2000 Received: from judy.ic.ac.uk (judy.ic.ac.uk [155.198.5.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA00808 for ; Fri, 11 Feb 2000 14:53:59 -0500 Received: from juliet.ic.ac.uk ([155.198.5.4]) by judy.ic.ac.uk with esmtp (Exim 2.12 #1) id 12JL5D-0004y1-00 for chemistry@ccl.net; Fri, 11 Feb 2000 18:46:23 +0000 Received: from origin.ch.ic.ac.uk ([155.198.224.252] helo=chcmga.ch.ic.ac.uk) by juliet.ic.ac.uk with esmtp (Exim 2.12 #1) id 12JL58-0000Yz-00 for chemistry@ccl.net; Fri, 11 Feb 2000 18:46:18 +0000 Received: from rzepa.ch.ic.ac.uk ([155.198.224.86]) by chcmga.ch.ic.ac.uk with esmtp (Exim 2.02 #1) id 12JL5B-002WYi-00; Fri, 11 Feb 2000 18:46:21 +0000 Mime-Version: 1.0 X-Sender: rzepa@argon.ch.ic.ac.uk Message-Id: In-Reply-To: References: Date: Fri, 11 Feb 2000 18:44:33 +0000 To: chemistry@ccl.net From: "Rzepa, Henry" Subject: XML (was From Your Coordinator: Anybody agrees with me? ) Content-Type: text/plain; charset="us-ascii" > PLEASE VISIT the: > http://www.xml-cml.org/ >... Please visit http://www.xml-cml.org/ (Yes, I have nothing to do with them). Since Jan has been kind enough to note the above site, I should also note the excellent series of tutorials on XML, and related aspects, by Miloslav Nic (an organic chemist!) http://zvon.vscht.cz/ZvonHTML/Zvon/zvonTutorials_en.html In another (this time shameless) plug, might I note that Chemint2000 (http://www.chemint.org/ ) in September of this year in Washington DC, will have a session on the application of XML and its relevance to chemistry. We anticipate that Peter Murray-Rust, Miloslav and myself, amongst others, will lead the discussions! Book now for a place!!! (sorry Jan). Finally, on the aspect of interconverting marked up chemical information components, and legacy program outputs, we are in the process of building a library of what we call XSL template fragments. These are used to build formal stylesheet transforms for interconverting XML/CML and such legacy outputs. We would expect the library to be modular and interchangeable. If you don't like the GUI, change the stylesheet! Please contact me for further details. Henry Rzepa. +44 (0)20 7594 5774 (Office) +44 (0)20 7594 5804 (Fax) Dept. Chemistry, Imperial College, London, SW7 2AY, UK. http://www.ch.ic.ac.uk/rzepa/ From chemistry-request@server.ccl.net Fri Feb 11 17:41:23 2000 Received: from lauca.usach.cl (lauca.usach.cl [158.170.64.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA02328 for ; Fri, 11 Feb 2000 17:41:20 -0500 Received: from localhost (fgonzale@localhost) by lauca.usach.cl (8.9.1b+Sun/8.9.2) with ESMTP id SAA09993 for ; Fri, 11 Feb 2000 18:32:55 -0300 (CDT) Date: Fri, 11 Feb 2000 18:32:55 -0300 (CDT) From: Fdo Danilo Gonzalez Nilo To: chemistry@ccl.net Subject: CNS: ATP..? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all! Im working with CNSsolve 1.0.... and I trying to make the .pdb and .mtf files for a protein-ATP complex. ... well,.. the question is: Anybody have the topology and parameter files to ATP?... or some solution for this problem? Thanks a lot!! Fernando Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology, Computational Chemistry Lab. Casilla 40, Correo 33, Santiago, Chile Fono: (562) 681 1542 Anexo:799 E-mail : fgonzale@lauca.usach.cl Fax : (562) 681 2108 ************************************************************************** From chemistry-request@server.ccl.net Fri Feb 11 17:43:22 2000 Received: from mail1.manquehue.net (mail1.manquehue.net [216.72.16.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA02348 for ; Fri, 11 Feb 2000 17:43:20 -0500 Received: from carlos (tc1-312.manquehue.net [216.72.18.55]) by mail1.manquehue.net (8.9.3/8.9.3) with ESMTP id SAA06481 for ; Fri, 11 Feb 2000 18:33:39 -0300 Message-Id: <200002112133.SAA06481@mail1.manquehue.net> From: "Carlos Robles V. " To: "=?ISO-8859-1?Q?Lista_de_Qu=EDmica?=" Subject: help me Date: Fri, 11 Feb 2000 18:31:36 -0600 X-MSMail-Priority: Normal X-Priority: 3 X-Mailer: Microsoft Internet Mail 4.70.1155 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi all, Anybody can tell me how can use the force fields files (for example MM3)? I need to know the bonds lenght, torsion angles, etc, but I don't know how . Thank in advance Carlos Robles