From chemistry-request@www.ccl.net Fri Apr 16 02:16:42 1999 Received: from postoffice.igalaxy.net ([207.126.82.14]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id CAA26752 Fri, 16 Apr 1999 02:16:41 -0400 (EDT) From: kaynjay@igalaxy.net Received: from kaynjay [207.126.85.6] by postoffice.igalaxy.net (SMTPD32-5.01) id A73926AD0328; Thu, 15 Apr 1999 23:22:49 PDT Date: Thu, 15 Apr 1999 23:08:49 -0700 To: CCL Subject: AutoDock and Linux (pentium) compilation? X-Mailer: MR/2 Internet Cruiser Edition for OS/2 v1.52 b52 Message-Id: <199904152322.SM00404@kaynjay> Hello, I am struggling to compile AutoDock 3.0 under Linux on our PC's and am getting errors about which I have no clue. I was wondering whether anyone has successfully compiled this on a similar system, what was used for the compiler options, and whether any system stuff should be installed beyond the normal compiler package? I am running Debian 2.1 with the 2.0.36 kernel and current ecgs C++ compiler. Thanks! Kenward Vaughan Bakersfield College -- ----------------------------------------------------------- kaynjay@igalaxy.net (home) kvaughan@bc.cc.ca.us (work) ----------------------------------------------------------- From chemistry-request@www.ccl.net Fri Apr 16 03:18:41 1999 Received: from uldns1.unil.ch (uldns1.unil.ch [130.223.8.20]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id DAA27119 Fri, 16 Apr 1999 03:18:40 -0400 (EDT) Received: from pcbch3207h.unil.ch ([130.223.143.63] ident=aborel) by uldns1.unil.ch with esmtp (Exim 2.12 #1) id 10Y2tX-0000JM-00; Fri, 16 Apr 1999 09:18:35 +0200 Message-ID: X-Mailer: XFMail 1.3 [p0] on Linux X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit MIME-Version: 1.0 In-Reply-To: <199904152322.SM00404@kaynjay> Date: Fri, 16 Apr 1999 09:18:34 +0200 (MET DST) Organization: Universiy of Lausanne Sender: aborel@pcbch3207h.unil.ch From: Alain Borel To: kaynjay@igalaxy.net Subject: RE: CCL:AutoDock and Linux (pentium) compilation? Cc: CCL On 16-Apr-99 kaynjay@igalaxy.net wrote: > Hello, > > I am struggling to compile AutoDock 3.0 under Linux on our PC's and am > getting errors about which I have no clue. I was wondering whether anyone > has successfully compiled this on a similar system, what was used for the > compiler options, and whether any system stuff should be installed beyond > the normal compiler package? > > I am running Debian 2.1 with the 2.0.36 kernel and current ecgs C++ > compiler. I don't know about AutoDock but I have some experience with building apps not explicitely supporting Linux. Could you tell me a bit more about the error message? ---------------------------------- E-Mail: Alain Borel Date: 16-Apr-99 Time: 09:17:17 From chemistry-request@www.ccl.net Fri Apr 16 05:29:20 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA27501 Fri, 16 Apr 1999 05:29:20 -0400 (EDT) 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 FAA05458; Fri, 16 Apr 1999 05:29:19 -0400 (EDT) Date: Fri, 16 Apr 1999 05:29:19 -0400 (EDT) From: Jan Labanowski To: chemistry@www.ccl.net cc: Jan Labanowski Subject: CCL Problems [From coordinator] Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I am very sorry for the mess which is currently with chemistry list. We are moving the whole operation to a totally different environment and different operating system (Solaris -> Linux). Things worked, when we did trials with 20 addresses. They do not work for 3000 addresses. You will, for a day or two, see the list unreliable. I am sorry for this, but at the same time this transition is inevitable and for better. I did not sleep for the last 3 days, so this message will be quite short (I do not see what I write anymore...). Now, all messages received, will be reposted, so please do not resend them. We are zooming on the problems, but unfortunately, they can only be tested under full load, and since I hate to be an experimental chemist (I prefer to be theoretical than computational {:-)}) and hate experimenting on people, I hope these convulsions will not take long. Sorry again Jan jkl@ccl.net 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 | From chemistry-request@www.ccl.net Fri Apr 16 07:25:47 1999 Received: from asp.biogeo.uw.edu.pl (grzesb@asp.biogeo.uw.edu.pl [148.81.33.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA28006 Fri, 16 Apr 1999 07:25:45 -0400 (EDT) Received: (from grzesb@localhost) by asp.biogeo.uw.edu.pl (8.8.7/8.8.7) id NAA29392; Fri, 16 Apr 1999 13:26:55 +0200 From: Grzegorz Bakalarski Message-Id: <199904161126.NAA29392@asp.biogeo.uw.edu.pl> Subject: G: G94 and new IBM AIX 4.3 (Power 2) To: chemistry@www.ccl.net Date: Fri, 16 Apr 1999 13:26:55 +0200 (EEST) Cc: grzesb@asp.biogeo.uw.edu.pl (Grzegorz Bakalarski) Content-Type: text Dear CCLers, I have a problem with installing G94 on a new IBM RS6K (Power 2) with AIX 3.2 and new compilers. The problem is that IBM made many changes in OS and compilers so I'm not not able to run binary code (exe) compiled on older machine & OS. G94 (D or E) almost compiles on a new machine (there are problems with fstatfs routine in mdutil.c). When I make neccessery changes I could compile to the end. However the code did not want to run - it stopped after reading link1 (%) lines of input. My question is: DID ANYBODY OF YOU SUCCEED IN COMPILING G94 ON RS6K WITH AIX 4.3 ? IF YES, COULD YOU SHARE NEEDED KNOWLEDGE HOW TO DO IT ? Thank a lot for any help. Regards, G.Bakalarski Warsaw University P.S. The latest supported AIX for G94 is probably 4.1.3! New G98 is ported to AIX 4.3, however changes in a code are significant ... I contacted with Gaussian and they don't plan to port G94 to new AIX, however say it should be possible .... From chemistry-request@www.ccl.net Fri Apr 16 09:10:21 1999 Received: from gatekeeper.eastman.com (gatekeeper.eastman.com [164.89.253.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA28693 Fri, 16 Apr 1999 09:10:20 -0400 (EDT) Received: by gatekeeper.eastman.com; id JAA19861; Fri, 16 Apr 1999 09:13:27 -0400 (EDT) Received: from emngw1.eastman.com(164.89.254.2) by gatekeeper.eastman.com via smap (3.2) id xma018767; Fri, 16 Apr 99 09:12:47 -0400 Received: by eastman.com id AA750430 (5.67b/IDA-1.5 for chemistry@www.ccl.net); Fri, 16 Apr 1999 09:09:09 -0400 Received: from ntmcon02.emn.com by eastman.com with SMTP id AA770904 (5.67b/SMI-4.1 for ); Fri, 16 Apr 1999 09:09:07 -0400 Received: by ntmcon02.emn.com with Internet Mail Service (5.5.2232.9) id <2WFLTBXP>; Fri, 16 Apr 1999 09:09:08 -0400 Message-Id: From: "Wilson, Bruce E" To: "'chemistry@www.ccl.net'" Subject: Summary: Plotting 2D or 3D data and seeing chemical structure Date: Fri, 16 Apr 1999 09:09:06 -0400 Mime-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2232.9) Content-Type: text/plain Several people responsed to my original request for information regarding software which would allow one to plot 2D or 3D data and easily see the chemical structures associated with data points. The results are summarized below. A number of people asked me to not use their names in any summary, so I've taken the liberty of summarizing responses, rather than including them explictly. 1) A number of people recommended the combination of Spotfire (http://www.spotfire.com) with Isis (http://www.mdli.com). A demo version of Spotfire can be downloaded from their web site, though that version doesn't have the structure capability in it. It does, however, illustrate the graphing and analysis capabilities of the software. Spotfire does, however, appear to be limited to 2D graphs. 2) A number of people also recommended Diva and/or Tsar, >from Oxford Molecular (http://www.oxmol.co.uk). Diva is the desktop product which has the graphics capabilities, while Tsar has the features for multivariate regression and QSAR type analysis. 3) Contrary to my original information and experience, it is possible to get at least close to what I was looking for with the MSI Cerius2 QSAR tools (http://www.msi.com). In particular, this requires turning on the label row by pickable and it appears to work best with the 3D plots, rather than 2D. 4) A few people also recommended the tools from Tripos (http://www.tripos.com), particulary the Tripos Molecular Spreadsheet and the HQSAR tools. 5) There is a project called CACTVS at the University of Erlangen (http://www2.ccc.uni-erlangen.de/software/cactvs/) which appears to be a toolkit by which one could get to any of a number of ends, including the ones I had in mind. At least on a first pass, it is not the most appropriate solution (yet) for my particular situation in an industrial environment with some very short deadlines. Anyone in academia or with a longer timescale, however, might do well to more seriously consider this toolkit. 6) This area appears to be one where there is also ongoing activity. I received a few responses from people who are doing development work in this area and who will likely have related products at some point in the future. Opinions and judgements expressed are my own, and I very much thank those who took the time to respond to my question. ====================================================== Bruce E. Wilson (bewilson@eastman.com) Eastman Chemical Company, Chemicals Research Division Lincoln St, B-150B, Box 1972 Kingsport, TN 37662-5150, USA Office: (423) 229-8886; FAX: (423) 229-4558 From chemistry-request@www.ccl.net Fri Apr 16 11:52:37 1999 Received: from MIT.EDU (SOUTH-STATION-ANNEX.MIT.EDU [18.72.1.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id LAA29631 Fri, 16 Apr 1999 11:52:36 -0400 (EDT) Received: from MASS-TOOLPIKE.MIT.EDU by MIT.EDU with SMTP id AA18977; Fri, 16 Apr 99 11:52:26 EDT Received: by mass-toolpike.mit.edu (8.8.7/4.7) id LAA04916; Fri, 16 Apr 1999 11:52:32 -0400 (EDT) Message-Id: <199904161552.LAA04916@mass-toolpike.mit.edu> To: chemistry@www.ccl.net Subject: sum: consistancy failure Date: Fri, 16 Apr 1999 11:52:32 EDT From: Ning Xie Hi, all, My thanks go to the people who replied my question. They are: 1. Doug Fox: gaussian.com!fox@lorentzian.com who suggested: "My best guess for the problem is that you will need a much better grid. Try INT=GRID=UltraFine."; 2. Peter Huesser who wrote: "I had the same problem a few years ago. If I remember right "SCF=NoVarrAcc" was the solution or Int=Rys1E or both."; 3. Han Zuilhof who wrote: "In our research on analogous polyDIacetylenes and oligomeric derivatives of this, convergence could -as in many other cases that one wants to study with large basis sets- be best achieved in a stepwise manner: start with a HF/3-21G single point, follow-up with guess=read with a B3LYP/6-31G* & loose scf criteria, and finish off with the B3LYP/6-311G** computation. (Do use the polarization functions, as the description will be significantly worse without them.) Once you have a B3LYP/6-311G** wavefunction on the starting geometry, our experience is that this will then rarely yield problems further on in the optimization in G94 (Gaussian 98 will likely be similar), even with much larger systems (upto C80)." and 4. Wai-To Chan who suggested: " Try the option scf=NoVarAcc to see if you can get around. If it is a single point calculation then specify scf=(NoVarAcc,tight). Note that tight is the default anyway for geometry optimisation. Hope this would solve your problem." The original question is: Hi, all, I'm trying to use BLYP/6-311g** to calculate the thermodynamic properties of polyacetylenes (C2H2 to C20H2 or even higher with respect to the number of carbons). The job is terminated shortly after it is started and gives a "consistency failure #2 in CalDSu" message in the log file. I changed the basis set to 6-311g and use SCF=QC and it still does not work. Any suggestion is appreciated. Thank you very much. Regards, ning The last part of the log file is Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Integral accuracy reduced to 1.0D-05 until final iterations. Problem detected with inexpensive integrals. Switching to full accuracy and repeating last cycle. Warning! Spurious integrated density: NE= 74 NElCor= 0 Integral= 0.00000 Tolerance=1.00D-03 Consistency failure #2 in CalDSu. Error termination via Lnk1e in /usr2/g98/l502.exe. Job cpu time: 0 days 0 hours 0 minutes 38.5 seconds. File lengths (MBytes): RWF= 19 Int= 0 D2E= 0 Chk= 1 Scr= 1 I applied a combination of the suggestions and it worked with C12. Neither suggestion worked alone though. Thanks again. ning