From chemistry-request@server.ccl.net Thu Jul 8 05:12:37 1999 Received: from LMSMRM ([202.127.25.133]) by server.ccl.net (8.8.7/8.8.7) with SMTP id FAA31445 for ; Thu, 8 Jul 1999 05:12:28 -0400 Received: from LMSMRM (localhost [127.0.0.1]) by LMSMRM (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id RAA07539 for ; Thu, 8 Jul 1999 17:03:06 +0900 Sender: user@iris.sipp.ac.cn Message-ID: <37845B35.41C6@iris.sipp.ac.cn> Date: Thu, 08 Jul 1999 17:03:01 +0900 From: maoxiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: question about the GAMESS-UK Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone: I am using GAMESS-UK to search transition state. I can view the break of the bonds in MOLDEN, but I do not know which kind of the energy the gamess-UK gave is important, which one is the activation energy of the reaction. I have ask someone nearby , he says that I should do IRC, I know it can be done in MOPAC, but my problem is how I can do it in GAMESS-UK, and how I can know the point of the transition state in the energy curve. Hope to hear from you soon. Many thanks. Regards, Mao ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Mao Xiang | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Thu Jul 8 05:13:17 1999 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA31465 for ; Thu, 8 Jul 1999 05:13:15 -0400 Received: from ruppert.phys.chemie.tu-muenchen.de by mailrelay2.lrz-muenchen.de; Thu, 8 Jul 1999 11:07:50 +0200 Received: from physik.tu-muenchen.de by ruppert.phys.chemie.tu-muenchen.de via ESMTP (940816.SGI.8.6.9/930416.SGI) id LAA09374; Thu, 8 Jul 1999 11:07:48 +0200 Sender: tmehnert@physik.tu-muenchen.de Message-Id: <37846A63.A8744025@physik.tu-muenchen.de> Date: Thu, 08 Jul 1999 11:07:48 +0200 From: Mehnert Thomas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: WeiQuan Tian , CHEMISTRY@ccl.net Subject: Re: CCL:Erroneous write. write -1 instead of 50250000 References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi altogether! There are several points to take into account in respect to your problems. 1) On several computer systems there were set certain limits for users especially if many people are working on such systems because the users have to divide the available resources. You can examine this possibility with "quota -v". 2) If you are working with NQS (Network Queuing System) you have to examine if there are some kinds of limitations. 3) Maybe you have some limitations for one file or one job setting with the order "limit". Generally, the error message: "Erroneous write. write -1 instead of 50250000" indicates a disk space problem and no memory problem. "write -1" means that the Computer could not write to a certain file since there are some limitations or your computer system has essentially not enough physical disk space. So your swap space of about 2GB will be useless concerning your actual problem. Frequency calculations and any kind of high level calculations such as QCISD or MP4 need a lot of disk space. For example your frequency calculation needs less than 200MB memory space for every pass but your disk space requirements will be possibly 30GB or more. Increase your disk space or reduce your level of calculations or your basis set and all your problems (no, of course only this problem) will disappear. Thomas Mehnert Tech. Univ. of Munich Germany > Hi, > > Maybe it is not only the problem for disk space. I did a calculation > C26H12O with 6-31G* by BLYP. I have 2 GB disk space for scratch file and I > am sure that this calculation doesn't need more than 2GB disk space. > However the job stopped at l1002 for the frequency calculation. So I guess > it is due to memory, however, I have 128MB memory in PII350 and I included > 120MB for the calculation. I was confused with this error. As in fact I > met the similar problem with UNIX, while I can't remember how I solved > such a problem. > > Wei Quan Tian > Univ. of GUelph > Canada > > > On Wed, 7 Jul 1999, Max Valdez wrote: > > > Hi everybody > > That kind of error is due because the disc has no more space to write on it. > > Make sure you will have enough space before you send that kind of calculation (or > > when the molecule is too large). i had the same problem a few days ago. > > > > I hope this helps > > Waves > > Max > > > > Sigismondo Boschi wrote: > > > > > Hi all, > > > > > > I have got some similar errors with g98 (A6) on an IBM SP Power3, > > > compiled with compiler version xlf 5.1. Is it an error due to the > > > impossibility of writing some files, or is it a gaussian error? > > > > > > I'm recompiling g98 (A7) with the new compiler, in order to see it changes > > > something. > > > > > > Thanks in advance. > > > > > > kind regards > > > > > > Sigismondo Boschi > > > > > > -------------------------- ------------------------- -------------------- > > > | | http://incm.cineca.it | | > > > | ------------ ------------ | > > > |Sigismondo Boschi |tel: +39 051 6171559 | > > > |CINECA (High Performance Systems) |fax: +39 051 6132198 | > > > |via Magnanelli, 6/3 |e-mail: s.boschi@cineca.it | > > > |40033 Casalecchio di Reno (BO)-ITALY | | > > > --------------------------------------- --------------------------------- > > > > > > On Wed, 7 Jul 1999, Qadir K. Timerghazin wrote: > > > > > > > Dear CCLers, > > > > > > > > Using G98w I often get such error during hi-level calcualtions (MP4, > > > > QCISD(T), etc.): > > > > > > > > Erroneous write. write -1 instead of 50250000. > > > > fd = 2 > > > > writwa > > > > > > > > What's is this? How to fix this problem? > > > > > > > > > > > > Best regards, > > > > Qadir Timerghazin mailto:qt@chat.ru > > > > > > > > > > > > > > > > > > > > > > > -= 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 Jul 8 06:10:53 1999 Received: from thewall.rsi.co.jp ([202.248.33.130]) by server.ccl.net (8.8.7/8.8.7) with SMTP id GAA32123 for ; Thu, 8 Jul 1999 06:10:51 -0400 To: chemistry@ccl.net Date: Thu, 8 Jul 1999 19:03:09 +0900 Subject: TD-DFT Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Message-ID: <492567A8.0037280F.00@cc.m-kagaku.co.jp> From: "Guillaumont 4405821 Dominique" <4405821@cc.m-kagaku.co.jp> X-Lotus-FromDomain: MCC@MCC_EXM Dear all, I would have 2 questions concerning TD-DFT method. I'm trying to calculate electronic excited states with TD-DFT implemented in gaussian for organic dyes with lowest excited states of clear valence type. My first question concerns the choice of the geometry, is it more justified to use an experimental geometry which should be closer to reality or to use a geometry optimized at the DFT level which should be more consistent with the calculations ? My second question concerns the choice of the functional, when going from a hybrid (B3P86, B3LYP) to a non-hybrid functional (BP86,BLYP), the energy are shifted from 1000 to 5000 cm-1, and also the relative order of some excited states change, especially for the triplet states.Hybrid functionals reproduce better experimental spectra but give too high energies for triplet states. Which are the reasons other than the correct reproduction of experimental datas to chose a functional ? Thanks in advance, Dominique Guillaumont 4405821@cc.m-kagaku.co.jp From chemistry-request@server.ccl.net Thu Jul 8 10:47:43 1999 Received: from inch.uia.ac.be (inch.uia.ac.be [143.169.4.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA03688 for ; Thu, 8 Jul 1999 10:47:40 -0400 Received: from uia.ac.be by inch.uia.ac.be; (8.8.8/1.1.8.2/22Feb95-0943AM) id QAA15823; Thu, 8 Jul 1999 16:42:10 +0200 (MET DST) Sender: roussea@uia.ua.ac.be Message-ID: <3784B569.51CC8045@uia.ac.be> Date: Thu, 08 Jul 1999 16:27:53 +0200 From: Bart Rousseau Organization: University of Antwerp (UIA) X-Mailer: Mozilla 4.06 [en] (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: CCL Subject: spectroscopic ground state of atoms Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Can anybody tell me how I can calculate the electron density of the spectroscopic ground state of an atom at the SCF and MP2 level with G94? Thanks in advance, Bart. -- Bart Rousseau, Ph.D. student University of Antwerp - Dep. of Chemistry Structural Chemistry - Quantum Chemistry http://sch-www.uia.ac.be/struct/quantum/ From chemistry-request@server.ccl.net Wed Jul 7 16:16:09 1999 Received: from sparrow.prod.itd.earthlink.net (cuckoo.prod.itd.earthlink.net [207.217.120.79]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA22436 for ; Wed, 7 Jul 1999 16:15:58 -0400 Received: from lrz.de (1Cust119.tnt1.rancho-cucamonga.ca.da.uu.net [208.251.225.119]) by sparrow.prod.itd.earthlink.net (8.9.3/8.9.3) with ESMTP id NAA13044; Wed, 7 Jul 1999 13:10:42 -0700 (PDT) Received: (from eugene.leitl@localhost) by lrz.de (8.8.8/8.8.8) id NAA08024; Wed, 7 Jul 1999 13:08:46 -0700 From: Eugene Leitl MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Date: Wed, 7 Jul 1999 13:08:45 -0700 (PDT) To: "Mackey, Mark" Cc: "'chemistry@ccl.net'" Subject: CCL:Java molecule viewer In-Reply-To: <199907070735.DAA10084@server.ccl.net> References: <199907070735.DAA10084@server.ccl.net> X-Mailer: VM 6.43 under 20.4 "Emerald" XEmacs Lucid Message-ID: <14211.45959.682070.291503@lrz.de> Mackey, Mark writes: > So, does anyone know if there is source code available for even a simple > molecule viewer? For portability reasons I would prefer code that works with > Java 1.1 or older: I've found a few molecule viewers (such as the > publically-released viewer from Tripos) but these all seem to require the > JDK 1.2 and Java3D extension. http://www.rahul.net/pcm/dismol/DisMol.html A freeware molecule display applet including source code If you have a Java-capable web browser, the DisMol applet should appear below. If you don't, you may find this page rather boring. This is a big applet, so it may take one or two minutes to load into your browser (sorry for the delay). If you see a molecule below, you can try rotating the molecule in various directions by dragging your mouse on the black background (be sure to hold down the mouse button while you do that). See the text window for other tricks. There are currently 2 molecules to choose from in the pulldown menu; the second one (from the IMM web site) can be pretty slow to download (240k) and display (several seconds to draw the entire molecule on a 300 mhz Pentium 2). If you install this on your own server, you will need to change the urls of the files to point to chemical files on your own server. I originally had an input window that allowed you to enter an arbitrary URL of a .pdb or .xyz to display. It wasn't usefull due to security restrictions on Java Applets. You get a security violation if you try to read a url that's not on the server that launched the applet. Send suggestions, comments or questions to Peter McCluskey. or post on the NanoCAD mailing list (send mail to Majordomo@world.std.com with "subscribe nanocad" in the body to subscribe). DisMol evolved from Will Ware's NanoCAD code and from Roger Sayle's RasMol code. If you're willing to do a little work installing RasMol, you can get much better control over how you see molecules with RasMol than with DisMol. Archives and precompiled executables Source file archives, these contain all the source files and compiled class files: DisMol.tar.gz Java source files. Most of the ones I've listed here are largely ported from RasMol's C code. (See also Will Ware's NanoCAD home page for other source files on which these depend): DisMol.java - the applet Element.java - standard atoms PDBAtom.java - generic subclass of class atom GenericGroup.java - adds some file-reading abilities to class group PDBGroup.java - some code for reading .pdb files XYZGroup.java - some code for reading .xyz files pdbreader.java - some code for reading .pdb files xyzreader.java - some code for reading .xyz files MaskDesc.java ResSynonym.java ShadeRef.java - code borrowed from RasMol for shading, fast rendering of atoms, bonds From chemistry-request@server.ccl.net Thu Jul 8 02:44:37 1999 Received: from onzon.univ-st-etienne.fr (onzon.univ-st-etienne.fr [161.3.1.35]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA28994 for ; Thu, 8 Jul 1999 02:44:37 -0400 Received: from specpc6.univ-st-etienne.fr (specpc6.univ-st-etienne.fr [161.3.2.106]) by onzon.univ-st-etienne.fr (8.8.8/jtpda-5.3) with SMTP id IAA02591 for ; Thu, 8 Jul 1999 08:39:15 +0200 (MET DST) Message-Id: <3.0.1.32.19990708083809.0080e420@onzon.univ-st-etienne.fr> X-Sender: jonin@onzon.univ-st-etienne.fr X-Mailer: Windows Eudora Pro Version 3.0.1 (32) [F] Date: Thu, 08 Jul 1999 08:38:09 +0100 To: chemistry@ccl.net From: christian Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi everyone, i am looking for a pseudopotential for the praseodyme (Pr3+) element, if anyone can give me some help. Thanks in advance From chemistry-request@server.ccl.net Thu Jul 8 03:31:01 1999 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by server.ccl.net (8.8.7/8.8.7) with SMTP id DAA30522 for ; Thu, 8 Jul 1999 03:30:57 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for CHEMISTRY@server.ccl.net id AA18079; Thu, 8 Jul 99 15:24:38 -0700 Date: Thu, 8 Jul 1999 15:24:38 -0700 (PDT) From: Fenglou Mao To: PDB List Cc: "CHEMISTRY@www.ccl.net" Subject: Binding database Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, I personally need a database to store binding information, and I think many other people need it, too. So I want to build a binding information database. At first, I want to survey the data I must collect, because I am not vey clear what kind of data other people want to use. I will write the data fields I will collect below, I am very glad if someone tell me anything I forgot. Thermodynamics data: 1. binding free energy. 2. binding entropy and enthalpy. 3. apparent rate constant. Experimental data: 1. temperature, pH, buffer and other components. 2. measurement method. Binding molecules: 1. structure data of two molecules before binding. 2. structure data of two molecules after binding. 3. interaction sites. 4. name of binding molecules. Verifying data: 1. name of author and submitter. 2. e-mail of author and submitter. 3. reference. Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 From chemistry-request@server.ccl.net Thu Jul 8 07:51:09 1999 Received: from cmcind.far.ruu.nl (cmcind.pharm.uu.nl [131.211.56.43]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA01300 for ; Thu, 8 Jul 1999 07:51:08 -0400 Received: from pharm.uu.nl (fischer.far.ruu.nl [131.211.56.46]) by cmcind.far.ruu.nl (980427.SGI.8.8.8/970903.SGI.AUTOCF) via ESMTP id NAA11188; Thu, 8 Jul 1999 13:44:08 +0200 (MDT) Sender: moret@pharm.uu.nl Message-ID: <37848F07.D49FA0C4@pharm.uu.nl> Date: Thu, 08 Jul 1999 13:44:07 +0200 From: "Ed E. Moret" Reply-To: E.E.Moret@pharm.uu.nl Organization: Utrecht University X-Mailer: Mozilla 4.61 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Mopac93 does not like my Zwitter ion Content-Type: multipart/mixed; boundary="------------ABDC798D7522E2B48B45DDB8" This is a multi-part message in MIME format. --------------ABDC798D7522E2B48B45DDB8 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCL While optimising my extended amino acid, 6-amino-hexanoic-acid, from this particular (attached file 6-AHA.mol2 or appended 6-AHA.dat) starting conformation with Mopac93 (AM1 PRECISE), the molecule folds and a proton jumps >from the amino-terminus to the carboxy-terminus. This result is rather dependent on the current starting geometry, so should not be considered too reliable, but still: is it possible that 6-AHA is not a Zwitter ion and the computation is correct? What experimental data to consult? Hopefully someone wants to have a look at these files and share his/her thoughts on this. With best regards Ed Moret PS 6-AHA.dat is appended below -- | Ed E. Moret (@more@) Department of Medicinal Chemistry | Faculty of Pharmacy Utrecht University The Netherlands | Tel.: +31 30 2536979(2536958) Fax: +31 30 2536655 | E-mail: E.E.Moret@pharm.uu.nl WWW: http://wwwcmc.pharm.uu.nl/moret/ T=3600 AM1 NOINTER BONDS PRECISE /mnt/edu/moret/6-AHA.dat 0001 5.1982 0001 0.3053 0001 -8.9626 0001 0000 0000 0000 0006 4.5965 0001 0.6742 0001 -8.1320 0001 0000 0000 0000 0001 4.8952 0001 1.6948 0001 -7.8928 0001 0000 0000 0000 0001 2.8093 0001 -0.3674 0001 -8.7654 0001 0000 0000 0000 0006 3.1080 0001 0.6532 0001 -8.5262 0001 0000 0000 0000 0001 2.9533 0001 1.2900 0001 -9.3972 0001 0000 0000 0000 0001 6.4582 0001 -0.8408 0001 -5.6370 0001 0000 0000 0000 0006 6.3035 0001 -0.2039 0001 -6.5080 0001 0000 0000 0000 0001 6.6022 0001 0.8167 0001 -6.2689 0001 0000 0000 0000 0001 4.2133 0001 0.1440 0001 -6.0716 0001 0000 0000 0000 0006 4.8150 0001 -0.2249 0001 -6.9023 0001 0000 0000 0000 0001 4.5163 0001 -1.2456 0001 -7.1414 0001 0000 0000 0000 0001 6.8555 0001 -1.7456 0001 -7.9203 0001 0000 0000 0000 0006 7.1530 0001 -0.7248 0001 -7.6808 0001 0000 0000 0000 0001 6.9994 0001 -0.0882 0001 -8.5522 0001 0000 0000 0000 0008 9.0112 0001 -0.2659 0001 -6.0538 0001 0000 0000 0000 0006 8.6404 0001 -0.7038 0001 -7.2868 0001 0000 0000 0000 0008 9.5843 0001 -1.1231 0001 -8.1717 0001 0000 0000 0000 0001 2.5728 0001 2.1184 0001 -7.1728 0001 0000 0000 0000 0001 2.4368 0001 0.5522 0001 -6.5758 0001 0000 0000 0000 0001 1.2961 0001 1.1397 0001 -7.6629 0001 0000 0000 0000 0007 2.2917 0001 1.1537 0001 -7.3992 0001 0000 0000 0000 --------------ABDC798D7522E2B48B45DDB8 Content-Type: text/plain; charset=us-ascii; name="6-AHA.mol2" Content-Transfer-Encoding: 7bit Content-Disposition: inline; filename="6-AHA.mol2" # # Creating user name: hermel InsightII # Creation time: Tue Jun 22 17:15:28 1999 @MOLECULE AHA 22 21 5 0 0 SMALL USER_CHARGES @ATOM 1 H22 5.1982 0.3053 -8.9626 H 1 ETHL1 0.1000 **** 2 C2 4.5965 0.6742 -8.1320 C.3 1 ETHL1 -0.2000 **** 3 H21 4.8952 1.6948 -7.8928 H 1 ETHL1 0.1000 **** 4 H11 2.8093 -0.3674 -8.7654 H 1 ETHL1 0.1000 **** 5 C1 3.1080 0.6532 -8.5262 C.3 1 ETHL1 0.2200 **** 6 H12 2.9533 1.2900 -9.3972 H 1 ETHL1 0.1000 **** 7 H21 6.4582 -0.8408 -5.6370 H 2 ETHL2 0.1000 **** 8 C2 6.3035 -0.2039 -6.5080 C.3 2 ETHL2 -0.2000 **** 9 H22 6.6022 0.8167 -6.2689 H 2 ETHL2 0.1000 **** 10 H11 4.2133 0.1440 -6.0716 H 2 ETHL2 0.1000 **** 11 C1 4.8150 -0.2249 -6.9023 C.3 2 ETHL2 -0.2000 **** 12 H12 4.5163 -1.2456 -7.1414 H 2 ETHL2 0.1000 **** 13 H12 6.8555 -1.7456 -7.9203 H 3 METH3 0.1000 **** 14 C1 7.1530 -0.7248 -7.6808 C.3 3 METH3 -0.2000 **** 15 H11 6.9994 -0.0882 -8.5522 H 3 METH3 0.1000 **** 16 O3 9.0112 -0.2659 -6.0538 O.2 4 CBXM4 -0.5700 **** 17 C1 8.6404 -0.7038 -7.2868 C.2 4 CBXM4 0.1400 **** 18 O2 9.5843 -1.1231 -8.1717 O.2 4 CBXM4 -0.5700 **** 19 H13 2.5728 2.1184 -7.1728 H 5 AMN45 0.3600 **** 20 H12 2.4368 0.5522 -6.5758 H 5 AMN45 0.3600 **** 21 H11 1.2961 1.1397 -7.6629 H 5 AMN45 0.3600 **** 22 N1 2.2917 1.1537 -7.3992 N.3 5 AMN45 -0.5000 **** @BOND 1 2 1 1 2 5 2 1 3 2 11 1 4 2 3 1 5 5 4 1 6 5 22 1 7 5 6 1 8 8 7 1 9 11 8 1 10 8 14 1 11 8 9 1 12 11 10 1 13 11 12 1 14 14 13 1 15 14 17 1 16 14 15 1 17 17 16 ar 18 17 18 ar 19 22 19 1 20 22 20 1 21 22 21 1 @SUBSTRUCTURE 1 ETHL1 1 **** 0 **** **** 2 ETHL2 7 **** 0 **** **** 3 METH3 13 RESIDUE 0 **** **** 4 CBXM4 16 **** 0 **** **** 5 AMN45 19 **** 0 **** **** --------------ABDC798D7522E2B48B45DDB8-- From chemistry-request@server.ccl.net Thu Jul 8 11:00:32 1999 Received: from mgcct6.nci.nih.gov (mgcct6.nci.nih.gov [137.187.211.216]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA03806 for ; Thu, 8 Jul 1999 11:00:31 -0400 Received: from helix.nih.gov (localhost [127.0.0.1]) by mgcct6.nci.nih.gov (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id MAA02763 for ; Thu, 8 Jul 1999 12:14:52 -0400 Sender: brunob@helix.nih.gov Message-ID: <3784CE7B.4C4B41B8@helix.nih.gov> Date: Thu, 08 Jul 1999 12:14:52 -0400 From: Bruno Bienfait Organization: National Cancer Institute X-Mailer: Mozilla 4.6 [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: Computer Chemistry List Subject: Problem with Macromodel on IRIX Content-Type: multipart/alternative; boundary="------------49B3B4DE6566A67F83569A15" --------------49B3B4DE6566A67F83569A15 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCL'ers, I am using Macromodel 6.0 on several SGI workstations. Surprisingly, the results obtained on a SGI Octane with IRIX 6.4 were different from those calculated on a Octane and an Origin both running IRIX 6.5. For instance, calculating the energy of cyclohexane (simply built using the GUI) afforded the following results (force field = MMFF, solvent =water): IRIX 6.4 machine: ENERGY: 37.03 kJ/mol ( 8.85 kcal/mol) Stretch: 15.62 Bend: 2.97 Prop Torsion: -11.85 Improp Torsion: 0.00 Electrostatic: 0.00 Cross Terms: -1.39 van der Waals: 24.17 Solvation: 7.50 Monitored BatchMin job completed. two IRIX 6.5 machines: ENERGY: 1.02 kJ/mol ( 0.24 kcal/mol) Stretch: 15.62 Bend: 2.97 Prop Torsion: -47.86 Improp Torsion: 0.00 Electrostatic: 0.00 Cross Terms: -1.39 van der Waals: 24.17 Solvation: 7.50 Monitored BatchMin job completed. I observed similar differences using the MM3* force field without solvent: IRIX 6.4 machine: ENERGY: 63.79 kJ/mol ( 15.25 kcal/mol) Stretch: 1.64 Bend: 0.42 Prop Torsion: 36.99 Improp Torsion: 0.00 Electrostatic: 0.00 Cross Terms: 0.08 van der Waals: 24.65 Solvation: 0.00 Monitored BatchMin job completed. two IRIX 6.5 machines: ENERGY: 33.93 kJ/mol ( 8.11 kcal/mol) Stretch: 1.64 Bend: 0.42 Prop Torsion: 7.13 Improp Torsion: 0.00 Electrostatic: 0.00 Cross Terms: 0.08 van der Waals: 24.65 Solvation: 0.00 Monitored BatchMin job completed. I suppose that the differences observed might be related to different shared librairies. Has anyone encountered such a problem before? Could someone confirm which one of the two output is the correct one? Thanks in advance. Bruno -- [ Bruno Bienfait, Ph. D. Laboratory of Medicinal Chemistry ] [ National Cancer Institute ] [ Email : brunob@helix.nih.gov National Institutes of Health ] [ Phone : (301) 402-3111 Building 37, Room 5B20 ] [ Fax : (301) 496-5839 Bethesda Maryland 20892 , USA ] [ WWW : http://www.brunob.org ] --------------49B3B4DE6566A67F83569A15 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit  
Dear CCL'ers,

I am using Macromodel 6.0  on several SGI workstations.  Surprisingly, the results obtained on a SGI Octane with IRIX 6.4  were different >from those calculated on a Octane and an Origin both running  IRIX 6.5.

For instance, calculating the energy of cyclohexane (simply built using the GUI) afforded the following results (force field = MMFF, solvent =water):
 
 

IRIX 6.4 machine:

ENERGY:       37.03 kJ/mol (        8.85 kcal/mol)
Stretch:          15.62  Bend:               2.97
Prop Torsion:    -11.85  Improp Torsion:     0.00
Electrostatic:     0.00  Cross Terms:       -1.39
van der Waals:    24.17  Solvation:          7.50
Monitored BatchMin job completed.

two IRIX 6.5 machines:

ENERGY:        1.02 kJ/mol (        0.24 kcal/mol)
Stretch:          15.62  Bend:               2.97
Prop Torsion:    -47.86  Improp Torsion:     0.00
Electrostatic:     0.00  Cross Terms:       -1.39
van der Waals:    24.17  Solvation:          7.50
Monitored BatchMin job completed.
 
 

I observed similar differences using the MM3* force field without solvent:

IRIX 6.4 machine:

ENERGY:       63.79 kJ/mol (       15.25 kcal/mol)
Stretch:           1.64  Bend:               0.42
Prop Torsion:     36.99  Improp Torsion:     0.00
Electrostatic:     0.00  Cross Terms:        0.08
van der Waals:    24.65  Solvation:          0.00
Monitored BatchMin job completed.
 
 

two IRIX 6.5 machines:

ENERGY:       33.93 kJ/mol (        8.11 kcal/mol)
Stretch:           1.64  Bend:               0.42
Prop Torsion:      7.13  Improp Torsion:     0.00
Electrostatic:     0.00  Cross Terms:        0.08
van der Waals:    24.65  Solvation:          0.00
Monitored BatchMin job completed.
 
 
 

I suppose that the differences observed  might be related to different shared librairies.
Has anyone encountered such a problem before? Could someone confirm which one of the two output is the correct one?

Thanks in advance.

Bruno
 
  

-- 
[ Bruno Bienfait, Ph. D.            Laboratory of Medicinal Chemistry ]
[                                   National Cancer Institute         ]
[ Email : brunob@helix.nih.gov      National Institutes of Health     ]
[ Phone : (301) 402-3111            Building 37, Room 5B20            ]
[ Fax   : (301) 496-5839            Bethesda Maryland 20892 , USA     ]
[ WWW   : http://www.brunob.org                                       ]
  --------------49B3B4DE6566A67F83569A15-- From chemistry-request@server.ccl.net Thu Jul 8 11:12:24 1999 Received: from galaad.citi2.fr (galaad.citi2.fr [192.70.98.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA03966 for ; Thu, 8 Jul 1999 11:12:24 -0400 Received: from bisance.citi2.fr (bisance.citi2.fr [192.70.98.30]) by galaad.citi2.fr (8.8.8/jtpda-5.3) with ESMTP id RAA24439 for ; Thu, 8 Jul 1999 17:06:57 +0200 (MET DST) Received: from (gresh@localhost) by bisance.citi2.fr (8.8.8/jtpda-5.3) id RAA16294 for chemistry@ccl.net; Thu, 8 Jul 1999 17:06:57 +0200 (MET DST) Date: Thu, 8 Jul 1999 17:06:57 +0200 (MET DST) From: gresh@citi2.fr (Nohad Gresh) Message-Id: <199907081506.RAA16294@bisance.citi2.fr> Content-Type: text Paris, 8 July, 1999 We would like to announce the availability at the Computational Chemistry List (ccl) of the SIBFA (Sum of Interactions Between Fragments Ab initio computed) procedure. It is at: http://www.ccl.net/cca/software/SOURCES/FORTRAN/sibfa/ and ftp://ftp.ccl.net/pub/chemistry/software/SOURCES/FORTRAN/sibfa/ SIBFA is molecular mechanics procedure which was formulated and calibrated on the basis of ab initio computations. Its purpose is the computation of inter- and intramolecular interactions involving molecules of biological interest, and molecules of interest in organic chemistry. The package includes the Fortran computer program, and several sample input data. Comments about the present package are welcome. Please address them to: Nohad Gresh Laboratoire de Pharmacochimie Moleculaire UMR 8600 CNRS, U266 INSERM 4, Avenue de l'Observatoire 75006 Paris, France. e-mail: gresh@bisance.citi2.fr Fax. 011 33 1 43 26 69 18 From chemistry-request@server.ccl.net Thu Jul 8 11:21:12 1999 Received: from smb.chem.niu.edu (smb.chem.niu.edu [131.156.9.3]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA04524 for ; Thu, 8 Jul 1999 11:21:12 -0400 Received: from smb by smb.chem.niu.edu via SMTP (940816.SGI.8.6.9/940406.SGI) id KAA11421; Thu, 8 Jul 1999 10:12:33 -0500 Sender: smb@smb.chem.niu.edu Message-ID: <3784BFE0.59E2@smb.chem.niu.edu> Date: Thu, 08 Jul 1999 10:12:32 -0500 From: Steven Bachrach X-Mailer: Mozilla 3.01 (X11; I; IRIX 5.3 IP12) MIME-Version: 1.0 To: computational chemistry list CC: CHMINF-L@LISTSERV.INDIANA.EDU Subject: IJC and Hackberry sites to move Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit At the end of July I will be taking a position at Trinity University in San Antonio, TX. The web servers that I manage will relocate with me to Texas. The NIU Cheminformatics Site (hackberry.chem.niu.edu) will be unavailable from July 26 to early in August. I will announce its reappearance in a variety of lists. The new URL for this site will be http://hackberry.chem.trinity.edu. All services currently available will continue after the move. The Internet Journal of Chemistry (www.ijc.com) will be unavailable from July 26 to early in August. Again, I will announce its reappearance via many email lists. The URL for the IJC will remain the same. I apologize in advance for any inconvenience this temporary interuption of services may have. After August 1, I can be reached at the following address: Department of Chemistry Trinity Unviersity 715 Stadium Drive San Antonio, TX 78212 Sincerely, Steve Bachrach -- Steven Bachrach Department of Chemistry and Biochemistry Northern Illinois University DeKalb, IL 60115 Phone: (815)753-6863 smb@smb.chem.niu.edu Fax: (815)753-4802 From chemistry-request@server.ccl.net Thu Jul 8 11:36:57 1999 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA04921 for ; Thu, 8 Jul 1999 11:36:57 -0400 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id LAA23866 for ; Thu, 8 Jul 1999 11:31:31 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <378220E7.A8E9EAD6@syr.edu> Date: Tue, 06 Jul 1999 11:29:43 -0400 From: Deepak Singh Organization: Dept. of Chem & Biochem, Syracuse University X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: Computational Chemistry List Subject: Ligand Docking Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi folks, I have a receptor all primed to dock a ligand. Thi sis my first ligand docking experience and I started looking in the literature for methodology. However, most of the literature I have found (mostly monte carlo based packages) use AMBER parameters. I havefound just one method based on CHARMM22 paramaters. Anyone has any insight into methods/algorithms/packages that can take a CHARMM crd or pdb file and use CHARMM rtf's and PARAM files to dock a ligand? Thanks Deepak. -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Thu Jul 8 12:11:53 1999 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA05439 for ; Thu, 8 Jul 1999 12:11:50 -0400 Received: from ruppert.phys.chemie.tu-muenchen.de by mailrelay2.lrz-muenchen.de; Thu, 8 Jul 1999 18:06:20 +0200 Received: from physik.tu-muenchen.de by ruppert.phys.chemie.tu-muenchen.de via ESMTP (940816.SGI.8.6.9/930416.SGI) id SAA09854; Thu, 8 Jul 1999 18:06:19 +0200 Sender: tmehnert@physik.tu-muenchen.de Message-Id: <3784CC7A.3F2AEEF7@physik.tu-muenchen.de> Date: Thu, 08 Jul 1999 18:06:19 +0200 From: Mehnert Thomas X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 5.3 IP22) MIME-Version: 1.0 To: Bart Rousseau , CCL Subject: Re: CCL:spectroscopic ground state of atoms References: <3784B569.51CC8045@uia.ac.be> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Bart! Here is your input-file: __________________________________________________________ %Chk=density %Mem=160MB #P RHF/3-21G Guess=(Only,Save) Test Density Calculations 0 1 O --link1-- %Chk=density #P RHF/3-21G Guess=Read Geom=AllCheck Cube=Density Density Test Density-File _______________________________________________________________ In my case I elected the oxygen atom, Method: RHF and the basis set 3-21G. The density values will be written into the Density-file named at the end of my example file. For further information you should read the GAUSSIAN User's Reference especially the sections of the keywords Cube and Density. Bye Thomas Bart Rousseau wrote: > Hi, > > Can anybody tell me how I can calculate the electron > density of the spectroscopic ground state of an atom > at the SCF and MP2 level with G94? > > Thanks in advance, > Bart. > > -- > Bart Rousseau, Ph.D. student > University of Antwerp - Dep. of Chemistry > Structural Chemistry - Quantum Chemistry > http://sch-www.uia.ac.be/struct/quantum/ > > -= 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 Jul 8 12:15:02 1999 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 MAA05578 for ; Thu, 8 Jul 1999 12:15:02 -0400 Received: from sandra.schrodinger.com (sandra.schrodinger.com [206.231.140.250]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id JAA32238; Thu, 8 Jul 1999 09:08:59 -0700 Received: from localhost (shenkin@localhost) by sandra.schrodinger.com (8.8.5/8.8.5) with ESMTP id MAA22856; Thu, 8 Jul 1999 12:07:04 -0400 X-Authentication-Warning: sandra.schrodinger.com: shenkin owned process doing -bs Date: Thu, 8 Jul 1999 12:07:04 -0400 (EDT) From: Peter Shenkin To: Bruno Bienfait cc: Computer Chemistry List Subject: Re: CCL:Problem with Macromodel on IRIX In-Reply-To: <3784CE7B.4C4B41B8@helix.nih.gov> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, There is a bug in the -mips4 fast math library (libfastm.so) originally distributed with IRIX 6.4 (and 6.3). This can be fixed by upgrading to IRIX 6.5, or by installing patch Patch 1774 or 3131 & 3219, or 2752. (Some of these may superceded; if so, install the later one(s). But your best bet is to upgrade. BTW, this is Q4.4 on our FAQ page, http://www.schrodinger.com/MacroModel/faq.html Hope this helps, -P. On Thu, 8 Jul 1999, Bruno Bienfait wrote: > > Dear CCL'ers, > > I am using Macromodel 6.0 on several SGI workstations. Surprisingly, > the results obtained on a SGI Octane with IRIX 6.4 were different from > those calculated on a Octane and an Origin both running IRIX 6.5. > > For instance, calculating the energy of cyclohexane (simply built using > the GUI) afforded the following results (force field = MMFF, solvent > =water): > > > > IRIX 6.4 machine: > > ENERGY: 37.03 kJ/mol ( 8.85 kcal/mol) > Stretch: 15.62 Bend: 2.97 > Prop Torsion: -11.85 Improp Torsion: 0.00 > Electrostatic: 0.00 Cross Terms: -1.39 > van der Waals: 24.17 Solvation: 7.50 > Monitored BatchMin job completed. > > two IRIX 6.5 machines: > > ENERGY: 1.02 kJ/mol ( 0.24 kcal/mol) > Stretch: 15.62 Bend: 2.97 > Prop Torsion: -47.86 Improp Torsion: 0.00 > Electrostatic: 0.00 Cross Terms: -1.39 > van der Waals: 24.17 Solvation: 7.50 > Monitored BatchMin job completed. > > > > I observed similar differences using the MM3* force field without > solvent: > > IRIX 6.4 machine: > > ENERGY: 63.79 kJ/mol ( 15.25 kcal/mol) > Stretch: 1.64 Bend: 0.42 > Prop Torsion: 36.99 Improp Torsion: 0.00 > Electrostatic: 0.00 Cross Terms: 0.08 > van der Waals: 24.65 Solvation: 0.00 > Monitored BatchMin job completed. > > > > two IRIX 6.5 machines: > > ENERGY: 33.93 kJ/mol ( 8.11 kcal/mol) > Stretch: 1.64 Bend: 0.42 > Prop Torsion: 7.13 Improp Torsion: 0.00 > Electrostatic: 0.00 Cross Terms: 0.08 > van der Waals: 24.65 Solvation: 0.00 > Monitored BatchMin job completed. > > > > > I suppose that the differences observed might be related to different > shared librairies. > Has anyone encountered such a problem before? Could someone confirm > which one of the two output is the correct one? > > Thanks in advance. > > Bruno > > > > -- > [ Bruno Bienfait, Ph. D. Laboratory of Medicinal Chemistry ] > [ National Cancer Institute ] > [ Email : brunob@helix.nih.gov National Institutes of Health ] > [ Phone : (301) 402-3111 Building 37, Room 5B20 ] > [ Fax : (301) 496-5839 Bethesda Maryland 20892 , USA ] > [ WWW : http://www.brunob.org ] > > > -- ********* Peter S. Shenkin; Schrodinger, Inc.; (201)433-2014 x111 ********* *********** shenkin@schrodinger.com; http://www.schrodinger.com *********** From chemistry-request@server.ccl.net Thu Jul 8 12:25:58 1999 Received: from inch.uia.ac.be (inch.uia.ac.be [143.169.4.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA05801 for ; Thu, 8 Jul 1999 12:25:54 -0400 Received: from uia.ac.be by inch.uia.ac.be; (8.8.8/1.1.8.2/22Feb95-0943AM) id SAA17702; Thu, 8 Jul 1999 18:20:27 +0200 (MET DST) Sender: roussea@uia.ua.ac.be Message-ID: <3784CC71.DAB7880D@uia.ac.be> Date: Thu, 08 Jul 1999 18:06:09 +0200 From: Bart Rousseau Organization: University of Antwerp (UIA) X-Mailer: Mozilla 4.06 [en] (X11; I; OSF1 V4.0 alpha) MIME-Version: 1.0 To: CCL Subject: spectroscopic state of an atom Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all, It seems that I was verry uncareful when writing my previous message to this list (included below). What I want to now is how to specify a specific state (in my case the spectroscopic ground state) for an atom in G94. Furthermore I don't want the density from G94 but the density matrix (from which I will calculate the denisty myself using another program). Original message: > > Can anybody tell me how I can calculate the electron > density of the spectroscopic ground state of an atom > at the SCF and MP2 level with G94? > Thanks, Bart. -- Bart Rousseau, Ph.D. student University of Antwerp - Dep. of Chemistry Structural Chemistry - Quantum Chemistry http://sch-www.uia.ac.be/struct/quantum/ From chemistry-request@server.ccl.net Thu Jul 8 13:21:49 1999 Received: from dulcinea.alcala.es (dulcinea.alcala.es [130.206.82.7]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA06538 for ; Thu, 8 Jul 1999 13:21:41 -0400 Received: from uni.alcala.es ([172.30.21.144]) by dulcinea.alcala.es (8.9.1/8.9.1) with ESMTP id TAA08070 for ; Thu, 8 Jul 1999 19:13:25 +0200 (MET DST) Sender: morreale@dulcinea.alcala.es Message-ID: <37855B19.CB12E236@uni.alcala.es> Date: Thu, 08 Jul 1999 19:14:50 -0700 From: antonio morreale Organization: Universidad de Alcala de Henares X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX 6.5 IP32) MIME-Version: 1.0 To: chemistry@ccl.net Subject: disks and g94 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear all, I'm having problems spliting scratch file over three disk when running MP2/6-31g* frecuency calculation. This is the rwf line I use, %rwf=/home3/scratch3/,8GB,/home2/scratch2/,7GB,/scratch/,1GB It is a big job that I run with 512 MB of memory. Two times has crashed because disk problems, when there is at least a total of 5 GB of space left. With this particular case this is the error I got while running l811.exe, Any hint would be very apreciate, Thanks, Antonio Morreale Internal consistency error detected in FileIO for unit 1 I= 7 J= 0. dumping /fiocom/, unit = 1 nfiles = 92 sizext = 524288 winblk = 512 defal = T lstwrd =********** number 0 0 0 0 0 0 0 base 687104 527872 675840 679936 294400 5053440********* end 689664 528384 679424 684544 294912 5136896********* end1 689664 528384 679424 684544 294912 5136896********* wr pntr 687104 527872 675840 679936 294400 5053440323777024 rd pntr 687104 527872 675840 679936 294400 5053440323777024 number 22 23 501 502 503 504 506 base 38264832 55438848 8192 14336 19456 5312000 227840 end 55438632125998848 9192 17086 27856 11381168 274091 end1 55438848125999104 9216 17408 28160 11381248 274432 wr pntr 38264832 55438848 8192 14336 19456 5312000 227840 rd pntr 38264832125998848 8192 14336 19456 5312000 274091 number 508 511 514 515 516 517 518 base 278016 140800 395264 294912 420352 520704 445440 end 278031 159329 420240 394816 445328 526725 520368 end1 278528 159744 420352 395264 445440 526848 520704 wr pntr 278016 140800 395264 294912 420352 520704 445440 rd pntr 278016 140800 395264 294912 420352 520704 445440 number 520 521 522 523 524 526 528 base 293888 526848 679424 527360 689664 5136896 739840 end 293893 526883 679870 527806 739393 5186625 764816 end1 294400 527360 679936 527872 739840 5187072 764928 wr pntr 293888 526848 679424 527360 689664 5136896 739840 rd pntr 293888 526848 679647 527360 739393 5136896 739840 number 530 532 534 536 538 545 547 base 528384 764928 553472 578560 603648 686592 686080 end 553360 789904 578448 603536 628624 686606 686500 end1 553472 790016 578560 603648 628736 687104 686592 wr pntr 528384 764928 553472 578560 603648 686592 686080 rd pntr 528384 764928 553472 578560 603648 686606 686080 number 548 551 552 559 562 565 569 base 628736 227328 226304 274944 159744 277504 685056 end 675566 227350 226320 274945 226092 277544 685057 end1 675840 227840 226816 275456 226304 278016 685568 wr pntr 628736 227328 226304 274944 159744 277504 685056 rd pntr 628736 227328 226304 274944 159744 277504 685056 number 571 575 577 579 580 581 582 base 5286912 29696 276480 226816 274432 276992 275968 end 5311888 140406 276501 226830 274656 277136 276303 end1 5312000 140800 276992 227328 274944 277504 276480 wr pntr 5286912 29696 276480 226816 274432 276992 275968 rd pntr 5286912 29696 276480 226816 274432 276992 275968 number 583 584 585 588 589 590 591 base 275456 278528 279040 840192 2863616 11381248 13404672 end 275470 278690 282361 2863248 4886672 13404304 14110272 end1 275968 279040 282624 2863616 4887040 13404672 14110720 wr pntr 275456 278528 279040 840192 2863616 11381248 13404672 rd pntr 275456 278528 279040 840192 2863616 11381248 13404672 number 592 593 594 596 598 603 606 base 14110720 18307072 16208896 20405248 17408 790016 684544 end 16208704 20405056 18306880 22503232 17410 839969 684768 end1 16208896 20405248 18307072 22503424 17920 840192 685056 wr pntr 14110720 18307072 16208896 20405248 17408 790016 684544 rd pntr 14110720 18307072 18306880 22503232 17408 790016 684544 number 607 619 631 634 651 654 655 base 685568 282624 4887040 5187072 22503424 26680832 4969984 end 685680 293822 4969698 5286530 26680660 28703888 4994960 end1 686080 293888 4969984 5286912 26680832 28704256 4995072 wr pntr 685568 282624 4887040 5187072 26680660 26680832 4969984 rd pntr 685568 282624 4887040 5187072 22503424 26680832 4969984 number 656 657 658 659 665 989 991 base 4995072 28704256 34236416 5028352 28160 9216 12288 end 5028001 34236328 38264465 5053328 29404 11716 13929 end1 5028352 34236416 38264832 5053440 29696 11776 14336 wr pntr 4995072 28704256 34236416 5028352 28160 9216 12288 rd pntr 4995072 28704256 34236416 5028352 28160 9216 13929 number 992 993 994 995 996 997 998 base 11776 7680 1024 7168 2048 2560 1536 end 11781 7690 1054 7178 2073 7064 1586 end1 12288 8192 1536 7680 2560 7168 2048 wr pntr 11776 7680 1024 7168 2048 2560 1536 rd pntr 11781 7690 1054 7178 2073 7064 1586 number 999 9993 9994 9995 9996 9997 9998 base 17920477692928281006592276829184274062848271296512130176512 end 19272*********477692592281006420276828884274062548271296512 end1 19456*********477692928281006592276829184274062848271296512 wr pntr 17920477692928281006592281006420276828884274062548271296512 rd pntr 17921477692928281006592277728320274062848271296512130176512 number 9999 base 125999104 end 130176340 end1 130176512 wr pntr130176340 rd pntr130176340 dumping /fiocom/, unit = 2 nfiles = 27 sizext = 0 winblk = 512 defal = F lstwrd = 620032 number 0 501 502 506 508 511 520 base 452703 100993 101993 104743 1024 150994 181264 end 620032 101993 104743 150994 1039 169523 181269 end1 620032 101993 104743 150994 1039 169523 181269 wr pntr 452703 100993 101993 104743 1024 150994 181264 rd pntr 452703 100993 101993 104743 1024 150994 181264 number 521 522 524 526 545 551 552 base 292018 1089 292067 341796 292053 181285 181269 end 292053 1535 341796 391525 292067 181307 181285 end1 292053 1535 341796 391525 292067 181307 181285 wr pntr 292018 1089 292067 341796 292053 181285 181269 rd pntr 292018 1089 292067 341796 292053 181285 181269 number 569 575 584 585 603 605 619 base 181307 181308 170767 170929 402750 402723 391525 end 181308 292018 170929 174250 452703 402750 402723 end1 181308 292018 170929 174250 452703 402750 402723 wr pntr 181307 181308 170767 170929 402750 402723 391525 rd pntr 181307 181308 170767 170929 402750 402723 391525 number 634 665 989 993 997 998 base 1535 169523 174250 176750 176760 1039 end 100993 170767 176750 176760 181264 1089 end1 100993 170767 176750 176760 181264 1089 wr pntr 1535 169523 174250 176750 176760 1039 rd pntr 1535 169523 174250 176750 176760 1039 dumping /fiocom/, unit = 3 nfiles = 1 sizext = 524288 winblk = 512 defal = T lstwrd = 66048 number 0 base 1024 end 66048 end1 66048 wr pntr 1024 rd pntr 1024 Error termination in NtrErr: NtrErr called from FIOCnC. From chemistry-request@server.ccl.net Thu Jul 8 13:32:23 1999 Received: from mail.chat.ru (gnu.chat.ru [212.24.32.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA06653 for ; Thu, 8 Jul 1999 13:31:59 -0400 Received: from [62.76.11.197] (helo=chat.ru) by mail.chat.ru with smtp (Exim 2.12 #3) id 112Hwi-000MrV-00 for CHEMISTRY@ccl.net; Thu, 8 Jul 1999 21:26:59 +0400 Date: Thu, 8 Jul 1999 23:06:49 +0500 From: "Qadir K. Timerghazin" X-Mailer: The Bat! (v1.036) S/N B2B97075 Reply-To: "Qadir K. Timerghazin" Priority: Normal Message-ID: <11963.990708@chat.ru> To: CHEMISTRY@ccl.net Subject: G98 "writwa" again Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, Some days ago I wrote: > Using G98w I often get such error during hi-level calcualtions (MP4, > QCISD(T), etc.): > > Erroneous write. write -1 instead of 50250000. > fd = 2 > writwa > > What's is this? How to fix this problem? Many people have replied me. The common answer is: "this error due to too small disk space for scratch files". I encountered this error many times before, and solved the problem by enlarging the disk space. But now, performing G2 calculation of CH3OClO I encountered "writwa" in the beginning of QCI step: #P Geom=AllCheck Guess=TCheck QCISD(T,E4T)/6-311G(d,p) I had free space large enough (>4 GB) and the rwf file was 1-1.5 GB after this crash. Then I write Tran=Conven: #P G2 maxdisk=4250MB Tran=Conven geom=check and QCI step passed without any problems! And the rwf file didn't exceed 2 GB! So, enigmatic "writwa" error doesn't appear only in the case of the lack of disk space. Later, this job produced error during #P Geom=AllCheck Guess=TCheck MP4/6-311G(2df,p) Could anyone explain this? Best regards, Qadir Timerghazin mailto:qt@chat.ru From chemistry-request@server.ccl.net Thu Jul 8 13:56:06 1999 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA06895 for ; Thu, 8 Jul 1999 13:56:06 -0400 Received: from ccshst01 (ccshst01.cs.uoguelph.ca [131.104.96.14]) by ccshst09.cs.uoguelph.ca (8.8.6 (PHNE_17135)/8.8.6) with SMTP id NAA14161; Thu, 8 Jul 1999 13:50:32 -0400 (EDT) Date: Thu, 8 Jul 1999 13:50:32 -0400 (EDT) From: WeiQuan Tian X-Sender: wtian@ccshst01 To: antonio morreale cc: chemistry@ccl.net Subject: Re: CCL:disks and g94 In-Reply-To: <37855B19.CB12E236@uni.alcala.es> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII from the input file for splitting rwfs. The size of the rwf may be too big for computer limit. As I know the largest file for 32 Bit computer is about 2.1GB, once the size is out of such limit. Then the job crashes. Wei Quan Tian Univ. of Guelph Canada On Thu, 8 Jul 1999, antonio morreale wrote: > Dear all, > > I'm having problems spliting scratch file over three disk when running > MP2/6-31g* frecuency calculation. This is the rwf line I use, > > %rwf=/home3/scratch3/,8GB,/home2/scratch2/,7GB,/scratch/,1GB > > It is a big job that I run with 512 MB of memory. Two times has crashed > because disk problems, when there is at least a total of 5 GB of space > left. > > With this particular case this is the error I got while running > l811.exe, > > Any hint would be very apreciate, > > Thanks, > > Antonio Morreale > > Internal consistency error detected in FileIO for unit 1 I= 7 J= 0. > > > > dumping /fiocom/, unit = 1 nfiles = 92 sizext = 524288 winblk = 512 > > defal = T lstwrd =********** > > number 0 0 0 0 0 0 0 > base 687104 527872 675840 679936 294400 5053440********* > end 689664 528384 679424 684544 294912 5136896********* > end1 689664 528384 679424 684544 294912 5136896********* > wr pntr 687104 527872 675840 679936 294400 5053440323777024 > rd pntr 687104 527872 675840 679936 294400 5053440323777024 > > number 22 23 501 502 503 504 506 > base 38264832 55438848 8192 14336 19456 5312000 227840 > end 55438632125998848 9192 17086 27856 11381168 274091 > end1 55438848125999104 9216 17408 28160 11381248 274432 > wr pntr 38264832 55438848 8192 14336 19456 5312000 227840 > rd pntr 38264832125998848 8192 14336 19456 5312000 274091 > > number 508 511 514 515 516 517 518 > base 278016 140800 395264 294912 420352 520704 445440 > end 278031 159329 420240 394816 445328 526725 520368 > end1 278528 159744 420352 395264 445440 526848 520704 > wr pntr 278016 140800 395264 294912 420352 520704 445440 > rd pntr 278016 140800 395264 294912 420352 520704 445440 > > number 520 521 522 523 524 526 528 > base 293888 526848 679424 527360 689664 5136896 739840 > end 293893 526883 679870 527806 739393 5186625 764816 > end1 294400 527360 679936 527872 739840 5187072 764928 > wr pntr 293888 526848 679424 527360 689664 5136896 739840 > rd pntr 293888 526848 679647 527360 739393 5136896 739840 > > number 530 532 534 536 538 545 547 > base 528384 764928 553472 578560 603648 686592 686080 > end 553360 789904 578448 603536 628624 686606 686500 > end1 553472 790016 578560 603648 628736 687104 686592 > wr pntr 528384 764928 553472 578560 603648 686592 686080 > rd pntr 528384 764928 553472 578560 603648 686606 686080 > > number 548 551 552 559 562 565 569 > base 628736 227328 226304 274944 159744 277504 685056 > end 675566 227350 226320 274945 226092 277544 685057 > end1 675840 227840 226816 275456 226304 278016 685568 > wr pntr 628736 227328 226304 274944 159744 277504 685056 > rd pntr 628736 227328 226304 274944 159744 277504 685056 > > number 571 575 577 579 580 581 582 > base 5286912 29696 276480 226816 274432 276992 275968 > end 5311888 140406 276501 226830 274656 277136 276303 > end1 5312000 140800 276992 227328 274944 277504 276480 > wr pntr 5286912 29696 276480 226816 274432 276992 275968 > rd pntr 5286912 29696 276480 226816 274432 276992 275968 > > number 583 584 585 588 589 590 591 > base 275456 278528 279040 840192 2863616 11381248 13404672 > end 275470 278690 282361 2863248 4886672 13404304 14110272 > end1 275968 279040 282624 2863616 4887040 13404672 14110720 > wr pntr 275456 278528 279040 840192 2863616 11381248 13404672 > rd pntr 275456 278528 279040 840192 2863616 11381248 13404672 > > number 592 593 594 596 598 603 606 > base 14110720 18307072 16208896 20405248 17408 790016 684544 > end 16208704 20405056 18306880 22503232 17410 839969 684768 > end1 16208896 20405248 18307072 22503424 17920 840192 685056 > wr pntr 14110720 18307072 16208896 20405248 17408 790016 684544 > rd pntr 14110720 18307072 18306880 22503232 17408 790016 684544 > > number 607 619 631 634 651 654 655 > base 685568 282624 4887040 5187072 22503424 26680832 4969984 > end 685680 293822 4969698 5286530 26680660 28703888 4994960 > end1 686080 293888 4969984 5286912 26680832 28704256 4995072 > wr pntr 685568 282624 4887040 5187072 26680660 26680832 4969984 > rd pntr 685568 282624 4887040 5187072 22503424 26680832 4969984 > > number 656 657 658 659 665 989 991 > base 4995072 28704256 34236416 5028352 28160 9216 12288 > end 5028001 34236328 38264465 5053328 29404 11716 13929 > end1 5028352 34236416 38264832 5053440 29696 11776 14336 > wr pntr 4995072 28704256 34236416 5028352 28160 9216 12288 > rd pntr 4995072 28704256 34236416 5028352 28160 9216 13929 > > number 992 993 994 995 996 997 998 > base 11776 7680 1024 7168 2048 2560 1536 > end 11781 7690 1054 7178 2073 7064 1586 > end1 12288 8192 1536 7680 2560 7168 2048 > wr pntr 11776 7680 1024 7168 2048 2560 1536 > rd pntr 11781 7690 1054 7178 2073 7064 1586 > > number 999 9993 9994 9995 9996 9997 9998 > base 17920477692928281006592276829184274062848271296512130176512 > end 19272*********477692592281006420276828884274062548271296512 > end1 19456*********477692928281006592276829184274062848271296512 > wr pntr 17920477692928281006592281006420276828884274062548271296512 > rd pntr 17921477692928281006592277728320274062848271296512130176512 > > number 9999 > base 125999104 > end 130176340 > end1 130176512 > wr pntr130176340 > rd pntr130176340 > > > dumping /fiocom/, unit = 2 nfiles = 27 sizext = 0 winblk = 512 > > defal = F lstwrd = 620032 > > number 0 501 502 506 508 511 520 > base 452703 100993 101993 104743 1024 150994 181264 > end 620032 101993 104743 150994 1039 169523 181269 > end1 620032 101993 104743 150994 1039 169523 181269 > wr pntr 452703 100993 101993 104743 1024 150994 181264 > rd pntr 452703 100993 101993 104743 1024 150994 181264 > > number 521 522 524 526 545 551 552 > base 292018 1089 292067 341796 292053 181285 181269 > end 292053 1535 341796 391525 292067 181307 181285 > end1 292053 1535 341796 391525 292067 181307 181285 > wr pntr 292018 1089 292067 341796 292053 181285 181269 > rd pntr 292018 1089 292067 341796 292053 181285 181269 > > number 569 575 584 585 603 605 619 > base 181307 181308 170767 170929 402750 402723 391525 > end 181308 292018 170929 174250 452703 402750 402723 > end1 181308 292018 170929 174250 452703 402750 402723 > wr pntr 181307 181308 170767 170929 402750 402723 391525 > rd pntr 181307 181308 170767 170929 402750 402723 391525 > > number 634 665 989 993 997 998 > base 1535 169523 174250 176750 176760 1039 > end 100993 170767 176750 176760 181264 1089 > end1 100993 170767 176750 176760 181264 1089 > wr pntr 1535 169523 174250 176750 176760 1039 > rd pntr 1535 169523 174250 176750 176760 1039 > > > dumping /fiocom/, unit = 3 nfiles = 1 sizext = 524288 winblk = 512 > > defal = T lstwrd = 66048 > > number 0 > base 1024 > end 66048 > end1 66048 > wr pntr 1024 > rd pntr 1024 > Error termination in NtrErr: > NtrErr called from FIOCnC. > > > > -= 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 Jul 8 14:34:51 1999 Received: from mailhost.det.ameritech.net (mpdr0.detroit.mi.ameritech.net [206.141.239.206]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA07475 for ; Thu, 8 Jul 1999 14:34:50 -0400 Received: from kressj.www.microsoft.com ([199.179.190.243]) by mailhost.det.ameritech.net (InterMail v4.01.01.00 201-229-111) with SMTP id <19990708182722.IVT26389.mailhost.det.ameritech.net@kressj.www.microsoft.com>; Thu, 8 Jul 1999 14:27:22 -0400 Message-ID: <006801bec96f$85299400$f3beb3c7@www.microsoft.com> Reply-To: "Jim Kress" From: "Jim Kress" To: "WeiQuan Tian" , "Max Valdez" Cc: "Sigismondo Boschi" , References: Subject: Re: CCL:Erroneous write. write -1 instead of 50250000 Date: Thu, 8 Jul 1999 14:27:21 -0400 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 If you are working with G98W on an NT system there are a number of undocumented file size limitations - some caused by NT, others caused by the G98W programmers. For example, with G98W you cannot have a read write file (rwf) that is larger than 2GB. You may see one that appears to be larger but G98W will crash if you continue the calculation. If you expect your rwf will need to be larger than 2GB you will need to use the multiple rwf option for G98W and specify multiple rwf files that are all LE 2GB (this is an undocumented 'feature' of G98W). Also, the maxdisk parameter cannot exceed 16GB due to 32 bit signed integer limitations in G98W. Also, when you specify multiple rwf files in G98W the rwf file names you use will interact with the other file names you specify for G98W so that the more rwf you specify the fewer characters you can use for other file names. In the limit of specifying 8 rwf files you will have no characters left over for file names of any other files you may want to specify in G98W. This is another undocumented 'feature' that G98W contains. Gaussian refuses to acknowledge these problems exist and they refuse to provide support for their resolution even though I have sent them sample data that conclusively demonstrates all these problems. This is one reason why I switched to GAMESS. Good luck. Jim Check out my web site http://www.kressworks.com/ It'll blow your mind (politically), stimulate your senses (artistically) and provide scientific insights that boggle the mind! ----- Original Message ----- From: WeiQuan Tian To: Max Valdez Cc: Sigismondo Boschi ; Sent: Wednesday, July 07, 1999 2:40 PM Subject: CCL:Erroneous write. write -1 instead of 50250000 > > Hi, > > Maybe it is not only the problem for disk space. I did a calculation > C26H12O with 6-31G* by BLYP. I have 2 GB disk space for scratch file and I > am sure that this calculation doesn't need more than 2GB disk space. > However the job stopped at l1002 for the frequency calculation. So I guess > it is due to memory, however, I have 128MB memory in PII350 and I included > 120MB for the calculation. I was confused with this error. As in fact I > met the similar problem with UNIX, while I can't remember how I solved > such a problem. > > Wei Quan Tian > Univ. of GUelph > Canada > > > On Wed, 7 Jul 1999, Max Valdez wrote: > > > Hi everybody > > That kind of error is due because the disc has no more space to write on it. > > Make sure you will have enough space before you send that kind of calculation (or > > when the molecule is too large). i had the same problem a few days ago. > > > > I hope this helps > > Waves > > Max > > > > Sigismondo Boschi wrote: > > > > > Hi all, > > > > > > I have got some similar errors with g98 (A6) on an IBM SP Power3, > > > compiled with compiler version xlf 5.1. Is it an error due to the > > > impossibility of writing some files, or is it a gaussian error? > > > > > > I'm recompiling g98 (A7) with the new compiler, in order to see it changes > > > something. > > > > > > Thanks in advance. > > > > > > kind regards > > > > > > Sigismondo Boschi > > > > > > -------------------------- ------------------------- -------------------- > > > | | http://incm.cineca.it | | > > > | ------------ ------------ | > > > |Sigismondo Boschi |tel: +39 051 6171559 | > > > |CINECA (High Performance Systems) |fax: +39 051 6132198 | > > > |via Magnanelli, 6/3 |e-mail: s.boschi@cineca.it | > > > |40033 Casalecchio di Reno (BO)-ITALY | | > > > --------------------------------------- --------------------------------- > > > > > > On Wed, 7 Jul 1999, Qadir K. Timerghazin wrote: > > > > > > > Dear CCLers, > > > > > > > > Using G98w I often get such error during hi-level calcualtions (MP4, > > > > QCISD(T), etc.): > > > > > > > > Erroneous write. write -1 instead of 50250000. > > > > fd = 2 > > > > writwa > > > > > > > > What's is this? How to fix this problem? > > > > > > > > > > > > Best regards, > > > > Qadir Timerghazin mailto:qt@chat.ru > > > > > > > > > > > > > > > > > > > > > > > > -= 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 > > > > ----- Original Message ----- From: WeiQuan Tian To: Max Valdez Cc: Sigismondo Boschi ; Sent: Wednesday, July 07, 1999 2:40 PM Subject: CCL:Erroneous write. write -1 instead of 50250000 > > Hi, > > Maybe it is not only the problem for disk space. I did a calculation > C26H12O with 6-31G* by BLYP. I have 2 GB disk space for scratch file and I > am sure that this calculation doesn't need more than 2GB disk space. > However the job stopped at l1002 for the frequency calculation. So I guess > it is due to memory, however, I have 128MB memory in PII350 and I included > 120MB for the calculation. I was confused with this error. As in fact I > met the similar problem with UNIX, while I can't remember how I solved > such a problem. > > Wei Quan Tian > Univ. of GUelph > Canada > > > On Wed, 7 Jul 1999, Max Valdez wrote: > > > Hi everybody > > That kind of error is due because the disc has no more space to write on it. > > Make sure you will have enough space before you send that kind of calculation (or > > when the molecule is too large). i had the same problem a few days ago. > > > > I hope this helps > > Waves > > Max > > > > Sigismondo Boschi wrote: > > > > > Hi all, > > > > > > I have got some similar errors with g98 (A6) on an IBM SP Power3, > > > compiled with compiler version xlf 5.1. Is it an error due to the > > > impossibility of writing some files, or is it a gaussian error? > > > > > > I'm recompiling g98 (A7) with the new compiler, in order to see it changes > > > something. > > > > > > Thanks in advance. > > > > > > kind regards > > > > > > Sigismondo Boschi > > > > > > -------------------------- ------------------------- -------------------- > > > | | http://incm.cineca.it | | > > > | ------------ ------------ | > > > |Sigismondo Boschi |tel: +39 051 6171559 | > > > |CINECA (High Performance Systems) |fax: +39 051 6132198 | > > > |via Magnanelli, 6/3 |e-mail: s.boschi@cineca.it | > > > |40033 Casalecchio di Reno (BO)-ITALY | | > > > --------------------------------------- --------------------------------- > > > > > > On Wed, 7 Jul 1999, Qadir K. Timerghazin wrote: > > > > > > > Dear CCLers, > > > > > > > > Using G98w I often get such error during hi-level calcualtions (MP4, > > > > QCISD(T), etc.): > > > > > > > > Erroneous write. write -1 instead of 50250000. > > > > fd = 2 > > > > writwa > > > > > > > > What's is this? How to fix this problem? > > > > > > > > > > > > Best regards, > > > > Qadir Timerghazin mailto:qt@chat.ru > > > > > > > > > > > > > > > > > > > > > > > > -= 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 Jul 8 14:35:33 1999 Received: from mailhost.det.ameritech.net (mpdr0.detroit.mi.ameritech.net [206.141.239.206]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA07509 for ; Thu, 8 Jul 1999 14:35:33 -0400 Received: from kressj.www.microsoft.com ([199.179.190.243]) by mailhost.det.ameritech.net (InterMail v4.01.01.00 201-229-111) with SMTP id <19990708182804.IWI26389.mailhost.det.ameritech.net@kressj.www.microsoft.com>; Thu, 8 Jul 1999 14:28:04 -0400 Message-ID: <007201bec96f$9e6f4e00$f3beb3c7@www.microsoft.com> Reply-To: "Jim Kress" From: "Jim Kress" To: "Qadir K. Timerghazin" , References: <11963.990708@chat.ru> Subject: Re: CCL:G98 "writwa" again Date: Thu, 8 Jul 1999 14:28:04 -0400 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 If you are working with G98W on an NT system there are a number of undocumented file size limitations - some caused by NT, others caused by the G98W programmers. For example, with G98W you cannot have a read write file (rwf) that is larger than 2GB. You may see one that appears to be larger but G98W will crash if you continue the calculation. If you expect your rwf will need to be larger than 2GB you will need to use the multiple rwf option for G98W and specify multiple rwf files that are all LE 2GB (this is an undocumented 'feature' of G98W). Also, the maxdisk parameter cannot exceed 16GB due to 32 bit signed integer limitations in G98W. Also, when you specify multiple rwf files in G98W the rwf file names you use will interact with the other file names you specify for G98W so that the more rwf you specify the fewer characters you can use for other file names. In the limit of specifying 8 rwf files you will have no characters left over for file names of any other files you may want to specify in G98W. This is another undocumented 'feature' that G98W contains. Gaussian refuses to acknowledge these problems exist and they refuse to provide support for their resolution even though I have sent them sample data that conclusively demonstrates all these problems. This is one reason why I switched to GAMESS. Good luck. Jim Check out my web site http://www.kressworks.com/ It'll blow your mind (politically), stimulate your senses (artistically) and provide scientific insights that boggle the mind! ----- Original Message ----- From: WeiQuan Tian To: Max Valdez Cc: Sigismondo Boschi ; Sent: Wednesday, July 07, 1999 2:40 PM Subject: CCL:Erroneous write. write -1 instead of 50250000 > > Hi, > > Maybe it is not only the problem for disk space. I did a calculation > C26H12O with 6-31G* by BLYP. I have 2 GB disk space for scratch file and I > am sure that this calculation doesn't need more than 2GB disk space. > However the job stopped at l1002 for the frequency calculation. So I guess > it is due to memory, however, I have 128MB memory in PII350 and I included > 120MB for the calculation. I was confused with this error. As in fact I > met the similar problem with UNIX, while I can't remember how I solved > such a problem. > > Wei Quan Tian > Univ. of GUelph > Canada > > > On Wed, 7 Jul 1999, Max Valdez wrote: > > > Hi everybody > > That kind of error is due because the disc has no more space to write on it. > > Make sure you will have enough space before you send that kind of calculation (or > > when the molecule is too large). i had the same problem a few days ago. > > > > I hope this helps > > Waves > > Max > > > > Sigismondo Boschi wrote: > > > > > Hi all, > > > > > > I have got some similar errors with g98 (A6) on an IBM SP Power3, > > > compiled with compiler version xlf 5.1. Is it an error due to the > > > impossibility of writing some files, or is it a gaussian error? > > > > > > I'm recompiling g98 (A7) with the new compiler, in order to see it changes > > > something. > > > > > > Thanks in advance. > > > > > > kind regards > > > > > > Sigismondo Boschi > > > > > > -------------------------- ------------------------- -------------------- > > > | | http://incm.cineca.it | | > > > | ------------ ------------ | > > > |Sigismondo Boschi |tel: +39 051 6171559 | > > > |CINECA (High Performance Systems) |fax: +39 051 6132198 | > > > |via Magnanelli, 6/3 |e-mail: s.boschi@cineca.it | > > > |40033 Casalecchio di Reno (BO)-ITALY | | > > > --------------------------------------- --------------------------------- > > > > > > On Wed, 7 Jul 1999, Qadir K. Timerghazin wrote: > > > > > > > Dear CCLers, > > > > > > > > Using G98w I often get such error during hi-level calcualtions (MP4, > > > > QCISD(T), etc.): > > > > > > > > Erroneous write. write -1 instead of 50250000. > > > > fd = 2 > > > > writwa > > > > > > > > What's is this? How to fix this problem? > > > > > > > > > > > > Best regards, > > > > Qadir Timerghazin mailto:qt@chat.ru > > > > > > > > > > > > > > > > > > > > > > > > -= 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 > > > > ----- Original Message ----- From: Qadir K. Timerghazin To: Sent: Thursday, July 08, 1999 2:06 PM Subject: CCL:G98 "writwa" again > Dear CCLers, > > Some days ago I wrote: > > Using G98w I often get such error during hi-level calcualtions (MP4, > > QCISD(T), etc.): > > > > Erroneous write. write -1 instead of 50250000. > > fd = 2 > > writwa > > > > What's is this? How to fix this problem? > Many people have replied me. The common answer is: "this error due to > too small disk space for scratch files". I encountered > this error many times before, and solved the problem by enlarging the disk > space. > But now, performing G2 calculation of CH3OClO I encountered "writwa" > in the beginning of QCI step: > > #P Geom=AllCheck Guess=TCheck QCISD(T,E4T)/6-311G(d,p) > > I had free space large enough (>4 GB) and the rwf file was 1-1.5 GB > after this crash. Then I write Tran=Conven: > > #P G2 maxdisk=4250MB Tran=Conven geom=check > > and QCI step passed without any problems! And the rwf file didn't exceed > 2 GB! So, enigmatic "writwa" error doesn't appear only in the case of > the lack of disk space. > > Later, this job produced error during > #P Geom=AllCheck Guess=TCheck MP4/6-311G(2df,p) > > > Could anyone explain this? > > Best regards, > Qadir Timerghazin mailto:qt@chat.ru > > > > -= 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 Jul 8 15:31:44 1999 Received: from carbon.chem.ucla.edu (carbon.chem.ucla.edu [128.97.35.55]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA08407 for ; Thu, 8 Jul 1999 15:31:43 -0400 Received: from red5 (pc-ll.chem.ucla.edu [128.97.35.245]) by carbon.chem.ucla.edu (8.9.1a/8.9.1) with SMTP id MAA28214; Thu, 8 Jul 1999 12:26:13 -0700 (PDT) Message-Id: <4.1.19990708122400.00deb6f0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Thu, 08 Jul 1999 12:33:03 -0700 To: "Jim Kress" , From: Laurence Lavelle Subject: Re: CCL:G98 "writwa" again In-Reply-To: <007201bec96f$9e6f4e00$f3beb3c7@www.microsoft.com> References: <11963.990708@chat.ru> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" See two comments below. At 02:28 PM 7/8/99 -0400, Jim Kress wrote: > >If you are working with G98W on an NT system there are a number of >undocumented file size limitations - some caused by NT, others caused by the >G98W programmers. > >For example, with G98W you cannot have a read write file (rwf) that is >larger than 2GB. You may see one that appears to be larger but G98W will >crash if you continue the calculation. Does this symptom also show up with G98W running indefinitely (CPU 100% use) and no progress ? >If you expect your rwf will need to >be larger than 2GB you will need to use the multiple rwf option for G98W and >specify multiple rwf files that are all LE 2GB (this is an undocumented >'feature' of G98W). As far as I know G98W does not allow multiple rwf files. If you have successfully done this I would appreciate knowing how. >Also, the maxdisk parameter cannot exceed 16GB due to >32 bit signed integer limitations in G98W. Also, when you specify multiple >rwf files in G98W the rwf file names you use will interact with the other >file names you specify for G98W so that the more rwf you specify the fewer >characters you can use for other file names. In the limit of specifying 8 >rwf files you will have no characters left over for file names of any other >files you may want to specify in G98W. This is another undocumented >'feature' that G98W contains. > >Gaussian refuses to acknowledge these problems exist and they refuse to >provide support for their resolution even though I have sent them sample >data that conclusively demonstrates all these problems. This is one reason >why I switched to GAMESS. > >Good luck. > > >Jim > >Check out my web site http://www.kressworks.com/ >It'll blow your mind (politically), stimulate your senses (artistically) >and provide scientific insights that boggle the mind! > >----- Original Message ----- >From: WeiQuan Tian >To: Max Valdez >Cc: Sigismondo Boschi ; >Sent: Wednesday, July 07, 1999 2:40 PM >Subject: CCL:Erroneous write. write -1 instead of 50250000 > > >> >> Hi, >> >> Maybe it is not only the problem for disk space. I did a calculation >> C26H12O with 6-31G* by BLYP. I have 2 GB disk space for scratch file and I >> am sure that this calculation doesn't need more than 2GB disk space. >> However the job stopped at l1002 for the frequency calculation. So I guess >> it is due to memory, however, I have 128MB memory in PII350 and I included >> 120MB for the calculation. I was confused with this error. As in fact I >> met the similar problem with UNIX, while I can't remember how I solved >> such a problem. >> >> Wei Quan Tian >> Univ. of GUelph >> Canada >> >> >> On Wed, 7 Jul 1999, Max Valdez wrote: >> >> > Hi everybody >> > That kind of error is due because the disc has no more space to >write on it. >> > Make sure you will have enough space before you send that kind of >calculation (or >> > when the molecule is too large). i had the same problem a few days ago. >> > >> > I hope this helps >> > Waves >> > Max >> > >> > Sigismondo Boschi wrote: >> > >> > > Hi all, >> > > >> > > I have got some similar errors with g98 (A6) on an IBM SP Power3, >> > > compiled with compiler version xlf 5.1. Is it an error due to the >> > > impossibility of writing some files, or is it a gaussian error? >> > > >> > > I'm recompiling g98 (A7) with the new compiler, in order to see it >changes >> > > something. >> > > >> > > Thanks in advance. >> > > >> > > kind regards >> > > >> > > Sigismondo Boschi >> > > >> > >> -------------------------- ------------------------- -------------------- >> > > | | http://incm.cineca.it | >| >> > > | ------------ ------------ >| >> > > |Sigismondo Boschi |tel: +39 051 6171559 >| >> > > |CINECA (High Performance Systems) |fax: +39 051 6132198 >| >> > > |via Magnanelli, 6/3 |e-mail: s.boschi@cineca.it >| >> > > |40033 Casalecchio di Reno (BO)-ITALY | >| >> > >> --------------------------------------- --------------------------------- >> > > >> > > On Wed, 7 Jul 1999, Qadir K. Timerghazin wrote: >> > > >> > > > Dear CCLers, >> > > > >> > > > Using G98w I often get such error during hi-level calcualtions (MP4, >> > > > QCISD(T), etc.): >> > > > >> > > > Erroneous write. write -1 instead of 50250000. >> > > > fd = 2 >> > > > writwa >> > > > >> > > > What's is this? How to fix this problem? >> > > > >> > > > >> > > > Best regards, >> > > > Qadir Timerghazin mailto:qt@chat.ru >> > > > >> > > >> > >> > >> > >> > >> > >> > >> > >> >> >> CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins >> 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 >> >> >> >> > > > >----- Original Message ----- >From: Qadir K. Timerghazin >To: >Sent: Thursday, July 08, 1999 2:06 PM >Subject: CCL:G98 "writwa" again > > >> Dear CCLers, >> >> Some days ago I wrote: >> > Using G98w I often get such error during hi-level calcualtions (MP4, >> > QCISD(T), etc.): >> > >> > Erroneous write. write -1 instead of 50250000. >> > fd = 2 >> > writwa >> > >> > What's is this? How to fix this problem? >> Many people have replied me. The common answer is: "this error due to >> too small disk space for scratch files". I encountered >> this error many times before, and solved the problem by enlarging the disk >> space. >> But now, performing G2 calculation of CH3OClO I encountered "writwa" >> in the beginning of QCI step: >> >> #P Geom=AllCheck Guess=TCheck QCISD(T,E4T)/6-311G(d,p) >> >> I had free space large enough (>4 GB) and the rwf file was 1-1.5 GB >> after this crash. Then I write Tran=Conven: >> >> #P G2 maxdisk=4250MB Tran=Conven geom=check >> >> and QCI step passed without any problems! And the rwf file didn't exceed >> 2 GB! So, enigmatic "writwa" error doesn't appear only in the case of >> the lack of disk space. >> >> Later, this job produced error during >> #P Geom=AllCheck Guess=TCheck MP4/6-311G(2df,p) >> >> >> Could anyone explain this? >> >> Best regards, >> Qadir Timerghazin mailto:qt@chat.ru >> >> >> >> CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins >> 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 >> >> >> >> > > > >-= 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 > > > > Laurence """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Department of Chemistry & Biochemistry and Molecular Biology Institute Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Office): (310) 825-2083 Room 3048A Young Hall Fax: (310) 206-4038 Phone (Lab): (310) 206-8270 Room 269B MBI http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""" From chemistry-request@server.ccl.net Thu Jul 8 15:47:59 1999 Received: from ccshst09.cs.uoguelph.ca (ccshst09.cs.uoguelph.ca [131.104.96.18]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA08635 for ; Thu, 8 Jul 1999 15:47:59 -0400 Received: from ccshst01 (ccshst01.cs.uoguelph.ca [131.104.96.14]) by ccshst09.cs.uoguelph.ca (8.8.6 (PHNE_17135)/8.8.6) with SMTP id PAA27996; Thu, 8 Jul 1999 15:42:26 -0400 (EDT) Date: Thu, 8 Jul 1999 15:42:26 -0400 (EDT) From: WeiQuan Tian X-Sender: wtian@ccshst01 To: Laurence Lavelle cc: Jim Kress , CHEMISTRY@ccl.net Subject: Re: CCL:G98 "writwa" again In-Reply-To: <4.1.19990708122400.00deb6f0@mbi.ucla.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII It's right that G98W does not allow the splitting of rwf files both in W9x and NT. One professor in my university called Gaussian Inc. for this matter. Wei Quan Tian From chemistry-request@server.ccl.net Thu Jul 8 16:03:42 1999 Received: from mailhost.det.ameritech.net (mpdr0.detroit.mi.ameritech.net [206.141.239.206]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA08840 for ; Thu, 8 Jul 1999 16:03:41 -0400 Received: from kressj.www.microsoft.com ([206.141.216.246]) by mailhost.det.ameritech.net (InterMail v4.01.01.00 201-229-111) with SMTP id <19990708195610.MEI26389.mailhost.det.ameritech.net@kressj.www.microsoft.com>; Thu, 8 Jul 1999 15:56:10 -0400 Message-ID: <001001bec97b$eca131e0$f6d88dce@www.microsoft.com> Reply-To: "Jim Kress" From: "Jim Kress" To: "WeiQuan Tian" , "Laurence Lavelle" Cc: References: Subject: Re: CCL:G98 "writwa" again Date: Thu, 8 Jul 1999 15:56:09 -0400 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Then your professor was misled. I have done it repeatedly on my NT machine. Here is an example: %Mem=438MB %rwf=K:\1\,2GB,K:\2\,2GB,K:\4\,2GB %nosave %chk=ne #MP4SDTQ (FULL)/AUG-cc-pV5Z 6D 10F guess=check scf=tight Neon dimer for MP4SDTQ and AUG-cc-pV5Z 0 1 Ne1 0. 0. 0. Ne2 0. 0. 2.4 the output file is attached. Also, look on page 10 of the G98W manual (manual version 6.0). Jim Check out my web site http://www.kressworks.com/ It'll blow your mind (politically), stimulate your senses (artistically) and provide scientific insights that boggle the mind! ----- Original Message ----- From: WeiQuan Tian To: Laurence Lavelle Cc: Jim Kress ; Sent: Thursday, July 08, 1999 3:42 PM Subject: Re: CCL:G98 "writwa" again > > It's right that G98W does not allow the splitting of rwf files both in > W9x and NT. 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hu, 8 Jul 1999 16:50:16 -0400 Received: from localhost (noronha@localhost) by dedalus.lcc.ufmg.br (8.9.3/8.9.3) with SMTP id RAA41170 for ; Thu, 8 Jul 1999 17:44:36 -0300 Date: Thu, 8 Jul 1999 17:44:35 -0300 (BSC) From: antonio luiz oliveira de noronha To: chemistry@ccl.net Subject: Membran Transport Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear ccl friends Some could give some references about membran transport. I intend to begin a work with this kind of simulations but I couldn't find any for beginners. Best Regards Antonio Luiz Oliveira de Noronha - noronha@dedalus.lcc.ufmg.br Quimica Medicinal de Organoestanicos NEQUIM - Nucleo de Estudos de Quimica Medicinal UFMG - Universidade Federal de Minas Gerais