From chemistry-request@server.ccl.net Thu Aug 1 22:33:45 2002 Received: from web12804.mail.yahoo.com ([216.136.174.39]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g722Xjf25995 for ; Thu, 1 Aug 2002 22:33:45 -0400 Message-ID: <20020802023345.77707.qmail@web12804.mail.yahoo.com> Received: from [203.87.150.242] by web12804.mail.yahoo.com via HTTP; Thu, 01 Aug 2002 19:33:45 PDT Date: Thu, 1 Aug 2002 19:33:45 -0700 (PDT) From: amor san juan Subject: Re: CCL:Segmentation fault error in Autodock To: "Herron, Steven" Cc: chemistry@ccl.net In-Reply-To: <4E4792C2A56F9242A6E1807025B2693E663DBE@e2k2.AD.FULLERTON.EDU> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Herron: If your platform is Linux, do stacksize unlimited by typing "ulimit -s 66666" in prompt area where your working. Segmentation fault crashed the program due to its small size. I experienced this before, and that is what I did. Amor --- "Herron, Steven" wrote: > > Dear CCLers, > > I need some help with autodock. I keep getting > a segmentation fault error when I run autodock. The > error only occurs when I use the genetic algorithm > and only on certain protein files. It is not the > ligand file because the ligand docks successfully > when I use a different protein. The protein and the > ligand dock successfully when I use the Simulated > Annealing algorithm, but I really like the Genetic > algorithm with a local search (GALS). I cannot > find the difference between the protein files that > run and the ones that don't. > I have also seen this occur when I try to add a > co-factor to the protein file. > > Any assistance is appreciated > > > Autodock runs initially but crashes once it starts > the genetic algorithm (as shown below) > > > >... > >... > BEGINNING LAMARCKIAN GENETIC ALGORITHM DOCKING > > Run: 1 / 10 > Updating Second Time-dependent Seed Now. > Seeds: 157989 1027642588 > Date: Thu Jul 25 17:16:28 2002 > > (this is the end of the output file) > > > Segmentation fault (core dumped) > > > Thanks in Advance, > > Steven R. Herron > sherron@fullerton.edu > > > -= This is automatically added to each message by > mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Fri Aug 2 00:13:12 2002 Received: from web12304.mail.yahoo.com ([216.136.173.102]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g724DCf28692 for ; Fri, 2 Aug 2002 00:13:12 -0400 Message-ID: <20020802041312.50238.qmail@web12304.mail.yahoo.com> Received: from [202.141.70.93] by web12304.mail.yahoo.com via HTTP; Thu, 01 Aug 2002 21:13:12 PDT Date: Thu, 1 Aug 2002 21:13:12 -0700 (PDT) From: Anirban Subject: CCL:DLPOLY(getting bad output )!! To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii hi!! I have been trying to run MD simulation using DLPOLY package for TIP4P water model. My initial configuration for TIP4P is the energy optimized coordinates of SPC/E model with the difference being that I add the coordinates of the massless site by calculating from the coordinates of oxygen and hydrogen atoms in SPC/E. Now the problem is that everytime I run the MD I get 'NANQ' for the energy and other terms in the OUTPUT file ,temperature becomes NANQ as well. Could someone please suggest what should I do to solve the problem . Do I have to generate the coordinates for TIP4P system from scratch or should I do something else ?? Thanks !! anirban __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Thu Aug 1 16:00:39 2002 Received: from dh094-210.csb.sunysb.edu ([129.49.94.210]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g71K0cf01391 for ; Thu, 1 Aug 2002 16:00:38 -0400 Received: from localhost (cuigl@localhost) by dh094-210.csb.sunysb.edu (8.11.6/8.11.6) with ESMTP id g71JoP003301 for ; Thu, 1 Aug 2002 15:50:25 -0400 X-Authentication-Warning: dh094-210.csb.sunysb.edu: cuigl owned process doing -bs Date: Thu, 1 Aug 2002 15:50:25 -0400 (EDT) From: "CUI, Guanglei" X-X-Sender: cuigl@dh094-210.csb.sunysb.edu To: chemistry@ccl.net Subject: compiling DOCK 4.0 under linux Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, all DOCK lovers, I wonder if anyone successfully compiled DOCK 4.0 under LINUX. I've tried a few times with different compilers. None worked. Various errors. I searched CCL for this topic and only saw questions but no replies. It seems DOCK only works on SGI machines after some tweaking. Any thoughts on that? Thanks in advance. -- Guanglei Cui Dept. of Chemistry SUNY at Stony Brook Stony Brook, NY 11790 From chemistry-request@server.ccl.net Fri Aug 2 03:36:26 2002 Received: from thor.chem.sdu.dk ([130.225.142.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g727aQf03118 for ; Fri, 2 Aug 2002 03:36:26 -0400 Received: from localhost (tetz@localhost) by thor.chem.sdu.dk (SGI-8.9.3/8.9.3) with ESMTP id JAA75912 for ; Fri, 2 Aug 2002 09:38:38 +0200 (MDT) Date: Fri, 2 Aug 2002 09:38:37 +0200 From: Per Tetzschner Olsen To: chemistry@ccl.net Subject: Problems with Linda in gaussian 98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL I have ran into a problem with g98. I am trying to use linda on a linux cluster, but I received an error after I submitted the job. I would appreciate any help. The submitted job: #! /bin/csh #PBS -l nodes=4 set node_list = '"'`cat $PBS_NODEFILE`'"' setenv GAUSS_LFLAGS "-nodelist $node_list" setenv g98root /usr/local/lib source $g98root/g98/bsd/g98.login setenv GAUSS_EXEDIR $g98root/g98 setenv GAUSS_SCRDIR /scratch setenv PATH ${PATH}":/usr/local/lib/g98/linda/intel-linux2.4/bin" /usr/local/lib/g98/bsd/g98l < /home/tetz/3mintpm3.inp > /home/tetz/3mintpm3.out I have used %nproclinda=4 instead of normal %nproc=4 in my .inp - file The error I received from my submitted job: setenv GAUSS_EXEDIR /usr/local/lib/g98/linda-exe:/usr/local/lib/g98 g98 /usr/local/lib/g98/linda-exe/l302.exel: error while loading shared libraries: util.so: cannot open shared object file: No such file or directory ntsnet: too many workers exited to continue ntsnet: needed: 3, started: 3, died: 1 first of all util.so exists in that library, so I believe could be an error loading the proper path but that is just a guess. the gaussian job crashes after l301, but that is no surprise. I hope someone can enlighten my unexperienced linda way With regards Per Tetzschner University of Southern Denmark 5230 Odense M Denmark From chemistry-request@server.ccl.net Fri Aug 2 11:31:45 2002 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g72FVjf18361 for ; Fri, 2 Aug 2002 11:31:45 -0400 Received: by mailbox.engr.sc.edu with Internet Mail Service (5.5.2656.59) id ; Fri, 2 Aug 2002 11:31:42 -0400 Message-ID: From: "WANG, YIXUAN " To: "'chemistry@ccl.net'" Subject: one output problem of G98 Date: Fri, 2 Aug 2002 11:31:39 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: text/plain; charset="iso-8859-1" Dear all, To optimize force fields we need the force constants in Cartesian coordinates. For the small molecules, G98 does give this output with #p, however there is no such output for the bigger molecules with more than 50 atoms. Does anybody know how to solve the problem? Thanks. Yixuan Wang Department of Chemical Engineering University of South Carolina Columbia, SC 29208 From chemistry-request@server.ccl.net Fri Aug 2 14:47:09 2002 Received: from wilson.acpub.duke.edu ([152.3.233.69]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g72Il9426402 for ; Fri, 2 Aug 2002 14:47:09 -0400 Received: from CONCORDIA (concordia.lib.duke.edu [152.16.191.233]) by wilson.acpub.duke.edu (8.12.4/8.12.4/Duke-5.0.0) with SMTP id g72Il7Eb026291; Fri, 2 Aug 2002 14:47:08 -0400 (EDT) X-Originating-IP: 152.3.169.5 X-Mailer: MyDuke.com X-Originator-Info: jz7@acpub From: To: Subject: Question about add parameters to Macromodel Date: Fri, 2 Aug 2002 14:44:32 -0400 Message-ID: <008901c23a54$a413a550$eabf1098@CONCORDIA> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Thread-Index: AcI6VKQRcHzDnJ3BQBGDS32vvR41UQ== Content-Class: urn:content-classes:message X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Virus-Scanned: by amavisd-milter, Duke University (http://amavis.org/) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g72Il9426403 Dear CCL, I'm now using Macromodel to do some energy minimization, and need to modify parameters in files mm3.fid and atom.typ. But I don't know how to do that. Will you help me with it? (The Macromodel is imbedded in Maestro software.) Thanks! From chemistry-request@server.ccl.net Fri Aug 2 11:54:32 2002 Received: from email.nist.gov ([129.6.2.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g72FsWf19564 for ; Fri, 2 Aug 2002 11:54:32 -0400 Received: from SILYL.nist.gov (silyl.nist.gov [129.6.194.163]) by email.nist.gov (8.12.2/8.12.2) with ESMTP id g72FsQ6o020310 for ; Fri, 2 Aug 2002 11:54:27 -0400 (EDT) Message-Id: <5.0.0.25.2.20020802112311.050e7d70@mailserver.nist.gov> X-Sender: rdj3@mailserver.nist.gov X-Mailer: QUALCOMM Windows Eudora Version 5.0 Date: Fri, 02 Aug 2002 11:54:17 -0400 To: CHEMISTRY@ccl.net From: Russ Johnson Subject: pyramidalization of amides Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hello, The NIST Computational Chemistry Comparison and Benchmark database (http://srdata.nist.gov/cccbdb) has experimental data and a bunch of calculations for a few amides: acetamide, urea, and version 7 (September 2002) will have experimental data as well for formamide and alanine. The pyramidalization can be compared at different levels of theory by looking a the HNCH dihedral, which is 180 degrees for a planar amide. The comparison can be set up in section IV.D.1 Hope this helps, Russ Johnson Dr. Russell D. Johnson III Research Chemist National Institute of Standards and Technology Computational Chemistry Group 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice 301+975-2513 fax 301+869-4020 email: russell.johnson@nist.gov From chemistry-request@server.ccl.net Fri Aug 2 15:47:29 2002 Received: from web20201.mail.yahoo.com ([216.136.226.56]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g72JlT428289 for ; Fri, 2 Aug 2002 15:47:29 -0400 Message-ID: <20020802194719.24486.qmail@web20201.mail.yahoo.com> Received: from [130.83.244.130] by web20201.mail.yahoo.com via HTTP; Fri, 02 Aug 2002 12:47:19 PDT Date: Fri, 2 Aug 2002 12:47:19 -0700 (PDT) From: Hatice Can Subject: Orbital symmetries To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear All, I did uhf calculations to chek the stability of wavefunction for the organic molecule when it is in gas phase or in supercage of zeolite using Gaussian 98. I have the response to confirm the wave function stability. Do I have to do wavefunction optimization with stable=opt keyword? My second question is to related orbital symmetries for that molecule. I could obtain the orbital symmetries for the molecule when it is gas phase, but in the case of supercage I can not have the orbital symmetries. If someone would like to explain this differences, I would be glad. All the suggestions and explanations will be summarised. __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Fri Aug 2 06:23:04 2002 Received: from uni-kl.de ([131.246.137.52]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g72AN3f07736 for ; Fri, 2 Aug 2002 06:23:03 -0400 Received: from mailgate2.uni-kl.de (mailgate2.uni-kl.de [131.246.120.7]) by uni-kl.de (8.12.4/8.12.4) with ESMTP id g72AN2lZ012997; Fri, 2 Aug 2002 12:23:02 +0200 (MET DST) Received: from aixs1.rhrk.uni-kl.de (exim@aixs1.rhrk.uni-kl.de [131.246.137.3]) by mailgate2.uni-kl.de (8.12.5/8.12.5) with ESMTP id g72AN2VY021848; Fri, 2 Aug 2002 12:23:02 +0200 Received: from aixd1.rhrk.uni-kl.de ([131.246.137.210] ident=exim) by aixs1.rhrk.uni-kl.de with esmtp (Exim 4.04) id 17aZaG-000Kw6-00; Fri, 02 Aug 2002 12:23:00 +0200 Received: from gerwalin (helo=localhost) by aixd1.rhrk.uni-kl.de with local-esmtp (Exim 3.03 #5) id 17aZaF-000JzY-00; Fri, 02 Aug 2002 12:22:59 +0200 Date: Fri, 2 Aug 2002 12:22:59 +0200 (MES) From: Elmar Gerwalin To: Matt Zwier cc: chemistry@ccl.net Subject: Re: CCL:Visualization of G98 normal modes In-Reply-To: <3D498360.9090902@hope.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Matt, > I'm working on looking at normal mode vibrations of fairly-complex dye > molecules. I'm currently using WebMO to view the FREQ calculation > output, and that works very well, but it cannot, for instance, animate > the motion of the molecule for each normal mode. Does anyone know of a > piece of software that can accomplish this? xvibs (simple "C" code, small binary, simply search thw www for it) can extract each normal mode from a g98 output and creates xyz-Files (which you can view with xmakemol or molden, e.g.) Bye Elmar ============================================================== Elmar Gerwalin , University of Kaiserslautern, Germany gerwalin@rhrk.uni-kl.de (soon: ) http://www.rhrk.uni-kl.de/~gerwalin ==============================================================