From chemistry-request@server.ccl.net Thu Jun 27 07:24:18 2002 Received: from hermes.csd.unb.ca (root@[131.202.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5RBOHW02420 for ; Thu, 27 Jun 2002 07:24:17 -0400 Received: from csd-dd0oht6l3yg (mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.9.3/8.9.3) with SMTP id IAA00254 for ; Thu, 27 Jun 2002 08:24:17 -0300 (ADT) Received: FROM pop.unb.ca BY csd-dd0oht6l3yg ; Thu Jun 27 08:23:40 2002 -0300 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.9.3/8.9.3) with ESMTP id IAA25016 for ; Thu, 27 Jun 2002 08:24:16 -0300 (ADT) X-WebMail-UserID: l72k6 Date: Thu, 27 Jun 2002 08:23:58 -0300 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: RE: CCL:Autodock - Integral Charges? Solution Message-ID: <3D17AB4D@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 Hello, I just wanted to thank everybody who replied to my question about integral charges in Autodock. As suggested by many, I examined the actual residues that were giving me problems and found many of them to be incompletely modelled (for example, a glutamate without a carboxylate group on the sidechain) or the bond order was wrong on some of the atoms. Modelling the complete amino acid or manipulating the charges on individual atoms corrects the problem. Again, thank you very much. Robert On Wed, 26 Jun 2002, Robert Flight wrote: > I just started using autodock, and I'm getting an error message about residues > not having integral charges. Does this mean that the charge on each peptide > of a receptor has to be an integral value of -1, 0, 1 or something along those > lines? As well, does anyone know how to avoid this problem, as it occurs > whether I calculate the charges in AutoDockTools or using another program > (Molecular Operating Environment - MOE). Any help or suggestions are > appreciated. > > Thanks, > > Robert > > Robert Flight > Department of Chemistry > University of New Brunswick > e-mail: L72K6@unb.ca > tel: 506-461-5760 > > > -= 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 > ******************************** Robert Flight Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6@unb.ca tel: (506) 461-5760 ******************************** From chemistry-request@server.ccl.net Thu Jun 27 08:09:51 2002 Received: from fyserv1.fy.chalmers.se ([129.16.110.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5RC9oW04336 for ; Thu, 27 Jun 2002 08:09:50 -0400 Received: from fy.chalmers.se (ftf-pc32.fy.chalmers.se [129.16.112.162]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id OAA08289; Thu, 27 Jun 2002 14:09:26 +0200 (MEST) Message-ID: <3D1B0116.6C4D1B3D@fy.chalmers.se> Date: Thu, 27 Jun 2002 14:12:06 +0200 From: Patrik Johansson Organization: CTH X-Mailer: Mozilla 4.51 [sv] (Win98; I) X-Accept-Language: sv MIME-Version: 1.0 To: chemistry@ccl.net, patrikj@fy.chalmers.se Subject: cat+an=salt reaction energies Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers I'm thinking of making calculations of the reaction energies (dE, dH, dG) for reactions of the type: Cat+ + An- <=> CatAn Cat+ will mainly be Li+. As it comes to choices of methods I'm not so clear on what is the preferred method: 1. Can G2/G3 type calculations be used? Should I then use ghost atoms to avoid BSSE (i.e. can G2/G3 use ghost atoms)? 2. Any other methods of preference? So far I've only used HF and B3LYP methods due to the sizes of the anions, but if significant improvements can be made with other methods... 3. Preferred basis sets? Any suggestions or pointers to relevant work much appreciated. best regards /Patrik -- Patrik Johansson (patrikj@fy.chalmers.se) Scientist @ Materials Physics Group Chalmers University of Technology 412 96 Goteborg SWEDEN NEW!!! http://fy.chalmers.se/mf/Computer.html http://fy.chalmers.se/~jpatrik/ From chemistry-request@server.ccl.net Thu Jun 27 02:43:06 2002 Received: from mail.chemie.fu-berlin.de (root@[160.45.24.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5R6h5W18046 for ; Thu, 27 Jun 2002 02:43:05 -0400 Received: from diels.chemie.fu-berlin.de ([160.45.24.148]) (1735 bytes) by mail.chemie.fu-berlin.de via sendmail with P:esmtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Thu, 27 Jun 2002 08:43:05 +0200 (CEST) (Smail-3.2.0.111) Date: Thu, 27 Jun 2002 08:43:00 +0200 From: Michael Patzschke To: chemistry@ccl.net Subject: US-GAMESS Hilderbrandt internals Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g5R6h6W18047 Hi, using the trudge-optimization or ghost-atoms with US-GAMESS requires the use of so called Hilderbrandt style internals. Even after reading the article recommended in the GAMESS input documentation R.L. Hilderbrandt, J.Chem.Phys. 51, 1654 (1969) the generation of the input file for larger molecules is still more or less a trial and error procedure. Does someone know of a better reference to this input-style or is someone aware of a program for doing the conversion at least semi-automatically ? If someone is unfamiliar with the name, here is an example for water (C2V): O 8. LC 0.00 0.0 0.00 - O K H 1. PCC 0.9626645 51.99673 0.00 + O K I Though this looks fairly simple it gets quite frustrating even for medium-sized molecules. Thank You, Michael ------------------------------------------------------------------------- Michael Patzschke | email: michaelp@chemie.fu-berlin.de Privat: | Freie Universität Berlin - Institut für Chemie Waghäuseler Str. 9/10 | Physikalische und Theoretische Chemie 10715 Berlin | Takustr. 3, 14195 Berlin, Germany ------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jun 27 04:18:48 2002 Received: from mailstudenti.unimi.it ([159.149.10.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5R8IlW25733 for ; Thu, 27 Jun 2002 04:18:47 -0400 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailstudenti.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0GYC00JS7V35LS@mailstudenti.unimi.it> for chemistry@ccl.net; Thu, 27 Jun 2002 10:18:41 +0200 (MEST) Received: from Villa (villa.farma.unimi.it [159.149.79.66]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with SMTP id <0GYC00MASV36Q2@smtp.unimi.it> for chemistry@ccl.net; Thu, 27 Jun 2002 10:18:42 +0200 (MEST) Date: Thu, 27 Jun 2002 10:22:07 +0200 From: Giulio Vistoli Subject: Re: CCL:free software for QM and MM calculations To: omar Deeb , chemistry@ccl.net Message-id: <001701c21db3$ba0a3da0$424f959f@Villa> Organization: =?iso-8859-1?Q?Universit=E0_di_Milano?= MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal References: <20020626084159.13044.qmail@web12307.mail.yahoo.com> Dear Omar Deeb In our website (http://users.unimi.it/~ddl) you can find the Win32 version of ORAC that is a program written by Procacci et al (http://linux0.chim.unifi.it/orac) for MM and MD simulations and you can find the optimized ORAC porting both for PentiumIV and for AMD Athlon. Moreover you can find our program VEGA to handle and analyze molecular structures that includes a graphical interface for MOPAC to do semiempirical calculations. Best regards Giulio Vistoli --------- Giulio Vistoli Istituto di Chimica Farmaceutica e Tossicologica Viale Abruzzi, 42 I-20131 Milano Italia Tel. +39-02-50317522 Fax +39-02-50317565 giulio.vistoli@unimi.it http://users.unimi.it/~ddl From chemistry-request@server.ccl.net Thu Jun 27 01:33:56 2002 Received: from hotmail.com ([64.4.15.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5R5XtW14130 for ; Thu, 27 Jun 2002 01:33:55 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 26 Jun 2002 22:33:49 -0700 Received: from 133.11.92.210 by lw10fd.law10.hotmail.msn.com with HTTP; Thu, 27 Jun 2002 05:33:49 GMT X-Originating-IP: [133.11.92.210] From: "warau kimura" To: chemistry@ccl.net Subject: Fwd: CPCM optimisation Date: Thu, 27 Jun 2002 14:33:49 +0900 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 27 Jun 2002 05:33:49.0781 (UTC) FILETIME=[37304850:01C21D9C] Hello, I am very thankful Dr.Emrys Thomas for replying my question about CPCM optimisation. I forward his answer here. Best wishes, Kimura From: E.W.Thomas@salford.ac.uk To: waraukimura@hotmail.com Subject: Re: CPCM optimisation Date: Wed, 26 Jun 2002 14:55:51 +0100 I have met this problem so many times (even with molecules < 15 atoms)that I do not regard CPCM as a viable model except of course for rigid geometries.Here is some advice I recieved recently: "When using CPCM one quite often run into optimisation problems dealing with more complex systems. You may overcome the problem by a partial optimisation followed by a full optimisation. Usually the convergence problem is related to the 'max force'. If this is the case then you can identify the degree of freedom, which is related to this max force. In the partial optimisation you should freeze this parameter - usually a dihedral angle. If the 'max force'is related to a heteroatom or chemical group it may be advantageous to freeze all geometric parameters related to this heteroatom or heavy atoms in the group. Sometimes this procedure requires a couple of partial optimisations but we succeeded in the end. If this doesn't help you may try to change different parameters related to the solvation model, e.g. increase the number of tesserae, change the partial charges (hereby change the atomic spheres) in an initial optimisation followed by an optimisation using default partial charges". In my experience the unsophisticated Onsager model in G98 always converges during optimisations.You could also check out GAMSOL3.0,which incorporates AMSOL into GAMESS(US) [with excellent documentation] and allows optimisations and frequency calculations at HF/6-31G* and HF/6-31+G* levels. Best wishes Emrys Thomas _________________________________________________________________ Get your FREE download of MSN Explorer at http://explorer.msn.com/intl.asp. From chemistry-request@server.ccl.net Thu Jun 27 04:14:26 2002 Received: from d12lmsgate.de.ibm.com ([195.212.91.199]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5R8EMW25295 for ; Thu, 27 Jun 2002 04:14:25 -0400 Received: from d12relay01.de.ibm.com (d12relay01.de.ibm.com [9.165.215.22]) by d12lmsgate.de.ibm.com (8.12.3/8.12.3) with ESMTP id g5R8E3g8047092; Thu, 27 Jun 2002 10:14:03 +0200 Received: from d13ml006 (d13ml006.ch.ibm.com [9.13.8.67]) by d12relay01.de.ibm.com (8.11.1m3/NCO/VER6.1) with ESMTP id g5R8B6a126398; Thu, 27 Jun 2002 10:11:06 +0200 Subject: CPMD V3.5.2 code To: cpmd-list@cpmd.org, simu@physinfo.ulb.ac.be, psik-network@dl.ac.uk, chemistry@ccl.net X-Mailer: Lotus Notes Build M12_02042002 Pre-release 1 February 04, 2002 Message-ID: From: "Alessandro Curioni" Date: Thu, 27 Jun 2002 10:11:04 +0200 X-MIMETrack: Serialize by Router on D13ML006/13/M/IBM(Release 5.0.9a |January 7, 2002) at 27/06/2002 10:11:06 MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Announcement: The updated version 3.5.2 of the CPMD program (ab-initio Molecular Dynamics program, developed by J. Hutter, M. Parrinello et al, copyright IBM Corp and MPI Stuttgart) is now available at www.cpmd.org. New Features included in the update are: -Interface to the new Vanderbilt pseudopotentials generation code. -Non Linear Core Correction (NLCC) with Vanderbilt pseudopotentials -Vanderbilt pseudopotentials bugs fixed -NEC optimization -General Fixes Any non-profit organization can obtain a free licence there. Thank you to everyone contributed to these new release!!! Your cpmd.org team. (www.cpmd.org) From chemistry-request@server.ccl.net Thu Jun 27 09:00:09 2002 Received: from chimfiz.icf.ro (postfix@[193.231.132.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5RD03W06593 for ; Thu, 27 Jun 2002 09:00:03 -0400 Received: from 127.0.0.1 (localhost [127.0.0.1]) by dummy.domain.name (Postfix on SuSE Linux 7.0 (i386)) with SMTP id 2BC5431175; Thu, 27 Jun 2002 15:00:25 +0300 (EEST) Received: by chimfiz.icf.ro (Postfix on SuSE Linux 7.0 (i386), from userid 1157) id 0AB9C31179; Thu, 27 Jun 2002 15:00:21 +0300 (EEST) Received: from localhost (localhost [127.0.0.1]) by chimfiz.icf.ro (Postfix on SuSE Linux 7.0 (i386)) with ESMTP id 080D031175; Thu, 27 Jun 2002 15:00:21 +0300 (EEST) Date: Thu, 27 Jun 2002 15:00:20 +0300 (EEST) From: Sorana IONESCU To: Michael Patzschke Cc: chemistry@ccl.net Subject: Re: CCL:US-GAMESS Hilderbrandt internals In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I've worked with Hildebrandt internals and it seems very difficult at the beginning. But it is not a problem to do it even for molecules with three aromatic rings. It is only a problem of getting used to it. I know no programmes to do it in your place. The inconvenient for me is that the GAMESS programme do not optimize more than ten parameters. If you have questions you could write me again. Good luck, Sorana ---------- Sorana Ionescu ROMANIAN ACADEMY PHYSICAL CHEMISTRY INSTITUTE 'I.G. Murgulescu' Quantum Chemistry Laboratory Splaiul Independentei 202, Bucharest 77208, ROMANIA Phone: 40.1.224.88.95 Fax: 40.1.312.11.47 Alternative e-mail: sorana@gw-chimie.math.unibuc.ro sorana@k.ro From chemistry-request@server.ccl.net Thu Jun 27 11:53:37 2002 Received: from mail.unimo.it ([155.185.1.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5RFraW14804 for ; Thu, 27 Jun 2002 11:53:37 -0400 Received: (from nobody@localhost) by mail.unimo.it (2.1.2/8.9.1/Execmail 2.1) id RAA675218; Thu, 27 Jun 2002 17:45:09 +0200 (CETDST) To: chemistry@ccl.net Subject: Sybyl_mol2 files for DOCK4.0 Message-ID: <1025192709.3d1b330503572@mail.unimo.it> Date: Thu, 27 Jun 2002 17:45:09 +0200 (CETDST) From: sarap@mail.unimo.it MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: IMP/PHP IMAP webmail program 2.2.4 Hello everybody, I've got a lot of questions for you! I'm a new Dock4.0 user, unfortunately I do not have access to the Sybyl suite of programs so I have to obtain mol2 files for docking in alternative ways. I've tried writing Sybyl_mol2 files with InsightII both for proteins (pdb files) and for ligands database (mdl files obtained by Catalyst and then convert in sd files by Babel). For the protein (I've selected Amber98 ff) the sybyl atom types were not correctly assigned (no N.4 atom type was assigned to the positively charged aminoacid according with the Tripos force field, carboxylic oxigen were labelled as O.2 instead of O.co2 and so on...) For the ligands databases in .sd format (cvff force field selected),often InsightII does not recognizes correctly the bond orders and consequently does not assigns proper charges and atom types. The automatic modification of bond orders within InsightII seems to me not to work well on all molecules. I have also encountered problems in assigning partial charges with cvff to positively charged molecules such as protonated triazine derivatives. My questions are: Do someone have similar problems? Is there an alternative procedure to obtain mol2 files appropriate for dock4.0? (mol2 files obtained by Babel lacks the SUBSTRUCTURE section which is required by dock4.0) Is there a way (a freeware script or something like that) to assign partial charges to a mol2 file obtained by the sdf2mol2 utility of dock? Have someone ever used the "chunks" executable of Dock to add Gasteiger-Marsili to mol2 files? Any suggestion would be appreciated, thank you in advance. Sara Pacchioni Sara Ph D Student Department of Medicinal Chemistry University of Modena And Reggio Emilia Via Campi 183 41100 Modena Italy +39-059-2055122 e-mail: pacchioni.sara@unimo.it From chemistry-request@server.ccl.net Thu Jun 27 10:39:14 2002 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5REdEW13267 for ; Thu, 27 Jun 2002 10:39:14 -0400 Received: from trentu.ca ([206.248.117.30]) by trentu.ca (PMDF V5.2-32 #37862) with ESMTP id <01KJF6W5Q8V800010A@trentu.ca> for chemistry@ccl.net; Thu, 27 Jun 2002 10:13:00 EST Date: Thu, 27 Jun 2002 10:14:49 -0400 From: elewars Subject: SUMMARY Semiempirical AIM To: chemistry@ccl.net Message-id: <3D1B1DD9.1BABFA24@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.79 [en] (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2002 June 27 Here is the summary (#1--#7, below); I thank all who responded. Basically: SE wavefunctions can't be used, at least not without modification, and at least not in the original Bader way, because they lack core orbitals (the SE basis set is a minimal valence set). For most chemistry core orbitals are not critical, but for AIM they are. Another possible problem is the small size of the wavefunction (roughly comparable to an STO-3G?). E. Lewars ========= Question 2002 June 23 Hello, Have there been attempts to use semiempirical wavefunctions (e.g. AM1, PM3) for, or as starting points for, AIM analysis? Thanks. E. Lewars ========================= Responses #1 Joel Foreman Hi, I'd be interested in any replies you get to this question. Thanks in advance. Dr Joel Foreman Department of Physics University of Durham UK ------------------ #2 Fernando Martin Hi, I also looked into that question a few years ago, but unfortunately I don't think one can generate the electron density from a wavefunction produced from a semiempirical Hamiltonian. I would very much appreciate it if you could summarize the answers you get. Thanks in advance, Fernando ------------------ #3 Dinamica Hello, There are a few problems here. One is that semi-empirical calculations describe only valence eletrons and AIM (as i know it) analysis should be performed with the full electron density. Another is the minimum basis set... It would be interesting to see if some kind of correction was used/tried regading the above problems, specially the absence of core density. Pls, let me know if you have answers regarding this. But topological analysis like AIM, can be performed in different types of densities/surfaces. greetings Guilherme ------------------------------------ IQUSP - Brasil -------------------- #4 "Fred P. Arnold" I don't have the reference handy, [He found it: J Comp Chem, 1996, 18, 416] but Gernot Frenking looked into AIM analysis from ECPs about 8 years ago. I'll dig for my folder tomorrow at work, if you're interested. He found (and I can concur from some work on Ruthenim silylenes) that not including the core density creates spurious critical points in the valence space. You can still integrate charges, however, if you eliminate the non-physical points. BCPs tend also to differ from their all electron counterparts. -Fred Frederick P. Arnold, Jr. NUIT, Northwestern U. f-arnold@northwestern.edu ----------------------- #5 Alan.Shusterman@directory.reed.edu (Alan Shusterman) I don't know of any attempts, but I'd be skeptical of such treatments for the following reasons: 1. There are no explicit core electrons in semi-empirical treatments 2. It is usually recommended that one use extended basis sets for AIM analyses, but semi-empirical wavefns, which are implicitly minimal basis, are usually expanded in the STO-3G basis 3. I have made visual comparisons of isodensity surfaces from AM1 and ab initio RHF models using Spartan, and while these surfaces are qualitatively similar at low density values, this is not the case for higher densities (> or =0.08 au). -Alan Alan Shusterman Department of Chemistry Reed College 3203 S.E. Woodstock Blvd. Portland, OR 97202 503-771-1112, ext. 7699 ----------------------------------------- #6 Victor Anisimov (Message 1) Hi, There are theoretical limitations on this way as semiempirical methods do not produce wavefunction and density matrix in normal quantum mechanical sense, i.e. in a numerical form. Thus, for example, there is no way to construct a wavefunction based on MO coefficients and Slater orbitals as one does in nonempirical methods, because atomic orbitals will be non-orthogonal but it is assumed by the NDDO approximation. The same is true for density matrix. The strength of semiempirical methods is in property prediction of molecular systems involving minimal computational power. While the aforementioned limitation exist no one can prevent from analysis of curvature of molecular electrostatic potential. With best regards, Victor Victor Anisimov FQS Poland, Fujitsu ul. Starowislna 13-15, 31-038 Krakow, Poland Email: victor@fqspl.com.pl Web: http://www.fqspl.com.pl Tel.(+48 12) 429-4345 Fax(+48 12) 429-6124 (Message 2) Rereading my message I have noticed an unclear statement regarding orthogonality, which I'd like to correct: > > Thus, for example, there is no way to construct a wavefunction based on MO > > coefficients and Slater orbitals as one does in nonempirical methods, > > because > > atomic orbitals will be non-orthogonal but it is assumed by the NDDO > > approximation. I intended to say that NDDO assumes AOs orthogonal, while Slater functions are not. Hence there is no way to construct a wavefunction. > > While the aforementioned limitation exist no one can prevent from analysis > > of curvature of molecular electrostatic potential. This is true of course starting from some distance from atomic centres, bigger than interatomic distance, which is out of interest of AIM. Bonding phenomenon in its full sense exist in the non-empirical framework only. Neglect of overlap results in some important terms missing in the Fockian and density matrix. Thus, for example, in order to get differential density in the NDDO framework the common procedure assumes renormalization of AOs which results in non-SCF density matrix. It would be quite risky to draw bonding conclusions from such density. Finally the conclusion is that NDDO methods can not be used for studying fine details of electronic distribution which are subject of AIM. Hope it helps. Best regards, Victor. ------------------ #7 "Bachrach, Steven" Dr. Lewars, You cannot do AIM analysis, at least in the way that Bader describes it with semiempirical wavefunctions because they do not have core orbitals. The density is actually dominated by the cores, especially near the nucleus and this gives rise to the atoms acting a local attractors. Without the cores, attractors may not appear at the nucleus. I tried this years ago. -- Steven Bachrach ph: (210)999-7379 Department of Chemistry fax: (210)999-7569 Trinity University 715 Stadium Drive San Antonio, TX 78212 steven.bachrach@trinity.edu ================================= ======================= ============== From chemistry-request@server.ccl.net Thu Jun 27 20:56:31 2002 Received: from TheWorld.com ([199.172.62.104]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5S0uVW05043 for ; Thu, 27 Jun 2002 20:56:31 -0400 Received: from vaio.theworld.com (1Cust191.tnt4.bos10.da.uu.net [63.10.168.191]) by TheWorld.com (8.9.3/8.9.3) with ESMTP id UAA06522 for ; Thu, 27 Jun 2002 20:56:26 -0400 Message-Id: <5.1.0.14.1.20020627210520.0239a220@pop.theworld.com> X-Sender: jle@pop.theworld.com X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 27 Jun 2002 21:06:11 -0400 To: chemistry@ccl.net From: Joe Leonard Subject: C Hacker question Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Folks, Does anybody know a way to determine the name of the calling routine from C - Routine A calls Routine B, and B wishes to know the name of whatever routine called it... If it's a real hack, something which works on Linux (or Linux and SGI) would do the trick. Pointers to these kinds of programmer tricks are appreciated as well! Thanks in advance! Joe Leonard jle@theworld.com (formerly jle@world.std.com) From chemistry-request@server.ccl.net Thu Jun 27 23:00:19 2002 Received: from odin.cair.du.edu ([130.253.1.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5S30JW08707 for ; Thu, 27 Jun 2002 23:00:19 -0400 Received: from CONVERSION-DAEMON.du.edu by du.edu (PMDF V6.1-1 #40620) id <0GYE09C01B0DRO@du.edu> for chemistry@ccl.net; Thu, 27 Jun 2002 21:00:13 -0600 (MDT) Received: from fermion ([130.253.177.56]) by du.edu (PMDF V6.1-1 #40620) with SMTP id <0GYE09J7KB0DNA@du.edu>; Thu, 27 Jun 2002 21:00:13 -0600 (MDT) Date: Thu, 27 Jun 2002 20:59:12 -0600 From: Jim Stoner Subject: G98 A11.1 and SMP under RedHat 2.4 To: chemistry@ccl.net Cc: help@gaussian.com Message-id: MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal Hi all Thanks for your time. I am having a killer of a time getting G98 to build with smp support. I am using the current version of PGI F77. The box I am using is a Dell Precision 530 w/ 1GB of RAM. The system environment is: # uname -a Linux strontium 2.4.9-21smp #1 SMP Thu Jan 17 14:01:48 EST 2002 i686 unknown Other applications compile and run under SMP with no problem. However, G98 kicks back the following in the logfile before it seg/malloc faults and core dumps from: # g98 ./2proctest.com ./ & [2] 1489 # shmget failed.: Invalid argument [2] Exit 1 g98 ./2proctest.com ./ # *********************************************** Gaussian 98: x86-Linux-G98RevA.11.1 1-Nov-2001 27-Jun-2002 *********************************************** %Chk=js3-5.chk %mem=50MB %NPROC=2 Will use up to 2 processors via shared memory. ------------------------- #P UHF/6-31G Opt PROP=epr ------------------------- 1/18=20,38=1/1,3; 2/9=110,17=6,18=5,40=1/2; 3/5=1,6=6,11=2,25=1,30=1/1,2,3; 4/7=2/1; 5/5=2,38=4/2; 6/7=2,8=2,9=2,10=2,17=2,26=4,28=1/1,2; 7//1,2,3,16; 1/18=20/3(1); 99//99; 2/9=110/2; 3/5=1,6=6,11=2,25=1,30=1/1,2,3; 4/5=5,7=2,16=2/1; 5/5=2,38=4/2; 7//1,2,3,16; 1/18=20/3(-5); 2/9=110/2; 6/7=2,8=2,9=2,10=2,17=2,19=2,26=4,28=1/1,2; 99/9=1/99; Leave Link 1 at Thu Jun 27 20:22:55 2002, MaxMem= 6553600 cpu: 0.1 If I try to specify 2 processors and worse, if I reduce the memory allocation even farther so it thinks it has enough, then it starts stating it is reducing the number of processors and evoking LINDA. Any ideas? Thanks again, Jim PS. Has anyone seen a substantial increases in production by envoking ATLAS instead of BLAS? Is it worth getting A11.3 for the ATLAS build? All thoughts would be gratefully appreciated... ===================================== James W. Stoner Doctoral Student University of Denver Department of Chemistry and Biochemistry Eaton Electron Paramagnetic Resonance Labs =====================================