From chemistry-request@server.ccl.net Mon Sep 27 03:37:07 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA24136 for ; Mon, 27 Sep 1999 03:37:07 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id DAA10127 for ; Mon, 27 Sep 1999 03:30:46 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id JAA23480; Mon, 27 Sep 1999 09:30:07 +0200 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: Mike Falcetta , chemistry@www.ccl.net Subject: Re: CCL:Linux distributions and FORTRAN (g77) Date: Mon, 27 Sep 1999 09:17:13 +0200 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <199909261946.OAA06478@kirk.anderson.edu> In-Reply-To: <199909261946.OAA06478@kirk.anderson.edu> MIME-Version: 1.0 Message-Id: <99092709300701.23454@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id DAA24137 On Son, 26 Sep 1999 Mike Falcetta wrote: >have considered RH 6.0, but have found the egcs g77 (which comes with RedHat) >gives me some problems (in particaular the code compiles fine, but gives >terribly wrong answers in several of my calculations, using the same inputs and >version of the program soem friends have obtained correct results so I am led to >the conclusion that it is likely the compilation/OS) ??? What exactly is calculated wrong (internally, not molcas results) ? Have you submitted a bug report yet ? We are using g77 on many machines, allmost all of which are running RedHat distributions. Most are upgraded to run gcc-2.95.1. And we are doing quite a bit of FORTRAN development (well, it's old code). There are no problems regarding correctness. >THus, my question is: Can anyone recommend a distribution of LINUX that comes >with a FORTRAN compiler that is fairly robust? Any Linux distribution + gcc-2.95.1 is doing well (Here and for others) ! -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Mon Sep 27 04:48:19 1999 Received: from ms.dicp.ac.cn ([159.226.159.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA24559 for ; Mon, 27 Sep 1999 04:47:35 -0400 Received: from p100 ([159.226.159.123]) by ms.dicp.ac.cn (8.8.5/SCO5) with SMTP id QAA29991 for ; Mon, 27 Sep 1999 16:37:03 +0800 (CST) Message-Id: <199909270837.QAA29991@ms.dicp.ac.cn> Date: Mon, 27 Sep 1999 16:45:45 +0800 From: Li Guo Hui To: "CHEMISTRY@ccl.net" Subject: how can translate C codes to FORTRAN codes? Organization: Dalian Institute of Chemical Physics X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear, CCLers: i want to translate some C or C++ codes to FORTRAN codes , but i donot know whethere it is exist.where can i get it? thanks in advance yours please reply with sslc@ms.dicp.ac.cn named Li. From chemistry-request@server.ccl.net Mon Sep 27 04:53:42 1999 Received: from ms.dicp.ac.cn ([159.226.159.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA24615 for ; Mon, 27 Sep 1999 04:51:44 -0400 Received: from p100 ([159.226.159.123]) by ms.dicp.ac.cn (8.8.5/SCO5) with SMTP id QAA00028 for ; Mon, 27 Sep 1999 16:39:51 +0800 (CST) Message-Id: <199909270839.QAA00028@ms.dicp.ac.cn> Date: Mon, 27 Sep 1999 16:48:33 +0800 From: Li Guo Hui To: "CHEMISTRY@ccl.net" Subject: how can translate C codes to FORTRAN codes? Organization: Dalian Institute of Chemical Physics X-mailer: FoxMail 3.0 beta 1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Dear, CCLers: i want to translate some C or C++ codes to FORTRAN codes with existing software, but i donot know whethere it is exist.where can i get it? thanks in advance yours please reply with sslc@ms.dicp.ac.cn named Li. From chemistry-request@server.ccl.net Mon Sep 27 06:12:56 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA24960 for ; Mon, 27 Sep 1999 06:12:56 -0400 Received: from vesta.tmf.bg.ac.yu (vesta.tmf.bg.ac.yu [147.91.42.100]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id GAA12038 for ; Mon, 27 Sep 1999 06:06:29 -0400 (EDT) Received: from elab.tmf.bg.ac.yu (peca.tmf.bg.ac.yu [147.91.40.35]) by vesta.tmf.bg.ac.yu (8.9.3/8.9.3) with ESMTP id MAA01606 for ; Mon, 27 Sep 1999 12:05:17 +0200 Message-ID: <37EF5025.D37B8265@elab.tmf.bg.ac.yu> Date: Mon, 27 Sep 1999 12:08:21 +0100 From: Stojakovic Djordje X-Mailer: Mozilla 4.03 [en] (WinNT; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: A Linux question Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CClers: I am a chemistry student using a Pentium PC under Red Hat Linux 5.0. Presently I have been trying to adapt a fortran source file written for the g77 compiler so that it could be compiled with the f2c compiler. In doing so I have encountered only one problem, and it refers to the g77's "loc" statement, as in the following program line: ifh=(ih-loc(fh(1)))/8+1 When I try to compile the source code with the f2c compiler, I get an error message saying "Undefined reference to 'loc_' ". My question is this: is there a statement in f2c that would be analogous to the statement "loc" in g77 ? I would be very grateful if you could help me with the problem. Greetings, Ana Bara --------------------------- Department of Chemistry University of Belgrade Belgrade, Yugoslavia E-mail: stojak@vesta.tmf.bg.ac.yu From chemistry-request@server.ccl.net Mon Sep 27 06:46:47 1999 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA25181 for ; Mon, 27 Sep 1999 06:46:45 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id MAA23725; Mon, 27 Sep 1999 12:38:07 +0200 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: Li Guo Hui , "CHEMISTRY@ccl.net" Subject: Re: CCL:how can translate C codes to FORTRAN codes? Date: Mon, 27 Sep 1999 12:36:04 +0200 X-Mailer: KMail [version 1.0.28] Content-Type: text/plain References: <199909270837.QAA29991@ms.dicp.ac.cn> In-Reply-To: <199909270837.QAA29991@ms.dicp.ac.cn> MIME-Version: 1.0 Message-Id: <99092712380603.23454@bacchus.pc1.uni-duesseldorf.de> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id GAA25188 On Mon, 27 Sep 1999 Li Guo Hui wrote: >i want to translate some C or C++ codes to FORTRAN codes , but i donot know whethere it >is exist.where can i get it? Are you sure ? Check news:comp.programmer.fortran (IIRC), there was some program called C2F posted/discussed several times. It's not very complete though. Actually many language constructs form C++ (and even C) don't translate to FORTRAN. So best would be to use the C++ code, or translate it manually :-( -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Mon Sep 27 08:15:19 1999 Received: from pub.jlonline.com. ([202.102.24.37]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA26295 for ; Mon, 27 Sep 1999 08:15:17 -0400 Received: from chungenl ([10.74.64.143]) by pub.jlonline.com. (8.9.1/8.9.1) with SMTP id UAA29646; Mon, 27 Sep 1999 20:02:51 +0800 (CST) Message-ID: <002301bf08e0$8b87e9e0$8f404a0a@chungenl> From: "Chungen Liu" To: "Bhupendra Wakankar" Cc: Subject: Summary:Help me on the selection of density functional and basis sets for transition metal compunds. Date: Mon, 27 Sep 1999 20:03:52 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear Bhupendra Wakankar, I am sorry for a delayed respond to your email. Now I have summarized all the answers to my question on the DFT calculation of the transition metal compounds. I would like to remind you of the names of those who were very kind to respond to my question. By the way, Do you have any idea of the basis set for Ce? Best regards Chungen. ---------------------------------------------------------------------------- --- Marcel Swart wrote: In general, GGA's (Becke-Perdew) give good results if used with a large enough basis set (at least TZP). I always use basis set IV in the ADF program (www.scm.com). M.Reinhold wrote: I think the choice of the DFT and the basis set you use depends very much on your system (e.g. if you ar e going to look at 1st, 2nd or 3rd row TM). There are some papers published by Tom Ziegler which might help you to find the right thing for you. I would not like to recommend anything, but maybe the most commonly used is the Becke Perdew gradient correction and the VWN method. Chaitanya Wannere wrote: As long as I know ppl around in our lab did some Transition metal calculations where they used the B3LYP method and for the metals I mean most of them they have a basis set if you are going to use the G-98 version of Gaussian. BUt if you are to use the G-94 version then you can get the basis sets of the metals which are effectively core potentials >from the Gaussian home page. Huajun wrote: I am not sure what you mean about "the selection of the density functional", but to select basis set, you have to create the basis set using the different diffuse atomic basis provide by density functional. I have used ADF package before. If you are using the same one, I might be able to provide more information for you. From chemistry-request@server.ccl.net Mon Sep 27 09:44:45 1999 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id JAA26855 for ; Mon, 27 Sep 1999 09:44:44 -0400 Received: from ren.tc.cornell.edu (REN.TC.CORNELL.EDU [128.84.20.129]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id JAA01947; Mon, 27 Sep 1999 09:37:21 -0400 Sender: richard@tc.cornell.edu Message-ID: <37EF7312.2781@tc.cornell.edu> Date: Mon, 27 Sep 1999 09:37:22 -0400 From: Richard Gillilan X-Mailer: Mozilla 3.01SC-SGI (X11; I; IRIX 6.2 IP22) MIME-Version: 1.0 To: sslc@ms.dicp.ac.cn CC: CHEMISTRY@ccl.net Subject: C to Fortran Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I may be wrong, but I suspect C and Fortran interconversion is a "one-way street". The man page for the f2c conversion says: "Some things are impossible to express in Fortran 77 or are harder to express in Fortran than in C (e.g. storage management, some character operations, arrays of functions, heterogeneous data structures, and calls that depend on the operating system) ..." C++ is even less likely to be convertable because its object-oriented nature would be awkward or even impossible to replicate in Fortran. It is possible to call Fortran routines from C programs (I have done it in the past). It is also possible to call C from Fortran. On SGI platforms, there is a program called "mkf2c" to create the appropriate wrappers for C code. Hope this helps Richard Gillilan Cornell Theory Center From tamasgunda@tigris.klte.hu Sun Sep 26 08:37:04 1999 -0400 Return-Path: Received: from tigris.klte.hu (tigris.klte.hu [193.6.138.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id IAA20173 for ; Sun, 26 Sep 1999 08:42:49 -0400 Message-Id: <199909261242.IAA20173@server.ccl.net> Received: from anti02 (193.6.134.181) by tigris.klte.hu (MX V5.1 Vn6f) with SMTP for ; Sun, 26 Sep 1999 14:33:23 +0200 From: "Tamas Gunda" To: chemistry@ccl.net Date: Sun, 26 Sep 1999 14:37:41 +1 Dear CCL Members, The new 3.40 version of the molecule file conversion, manipulation and utility program Mol2Mol is now available from CompuChem Ltd (http://www.compuchem.com/mol2mol.htm). The current version of Mol2Mol recognizes, and interconverts more than 30 different file formats. It contains a simple graphic display module to inspect the currently loaded molecule. It possesses some chemical intelligence for recognizing detailed atom types, hybridization and chemical environments, which is necessary for converting simpler formats (like X-ray crystallographic files) to more advanced ones, or when hydrogen atoms are automatically to be added to the heavy atoms. Most important features: Batch or many-to-many conversion; Conversion of multiple structural files; Conversion of proteins to "backbone molecules", Ramachandran plot; Manual editing of problematic files; Slicing of biopolymers and assemblies to individual molecules; Calculation of basic geometrical data: distances, angles, dihedral angles; Calculation of atom pyramidalities, angle of rings, distances from least square planes, ring puckerings; Change of bond types, atom types; Add or delete hydrogens, structural waters. New in Mol2Mol ver 3.40: New file formats have been added: MXYZ format read and write Gamess type Z-matrix and Cartesian (write) New features in the conversion: Support for PDB files containing only the backbone CA atoms; Support for PDB files with multiple structures (MODELS); New input and output variations have been added to the Cartesian format; Conversion of multi-structure files to multi-structure files are supported; The following formats have been upgraded and refined: Insight car Sybyl mol2 Macromodel PDB CSSR Z-matrix input, mainly Gaussian types POV-Ray files: Direct editing options of the povcolor.dat and *.pod include files have been added to the POV-Ray window; Support for the gradient fill coloring of the bonds; A few more color parameters are available in the povcolor.dat file; Support for the coloring according to atom charges or other atom properties inputted from data files; Support for the coloring according to residues, chains, models; Semitransparent filling of rings; Spline representation of peptide backbones. Centering of the molecule at chosen atoms is now possible; Coloring of the molecule according to models, chains, residues for better visualization (used in the POVRay format too). For more info see: http://www.compuchem.com/mol2mol.htm and/or http://dragon.klte.hu/~gundat/mol2mola.htm Demo version is downloadable. POV-Ray users may also have a look at: http://dragon.klte.hu/~gundat/povraya.htm (this link can be slow in the afternoons CET at workdays). From chemistry-request@server.ccl.net Mon Sep 27 09:44:20 1999 Received: from nwcst314.netaddress.usa.net (nwcst314.netaddress.usa.net [204.68.23.59]) by server.ccl.net (8.8.7/8.8.7) with SMTP id JAA26840 for ; Mon, 27 Sep 1999 09:44:19 -0400 Received: (qmail 2953 invoked by uid 60001); 27 Sep 1999 13:34:40 -0000 Message-ID: <19990927133440.2952.qmail@nwcst314.netaddress.usa.net> Received: from 204.68.23.59 by nwcst314 for [129.187.157.6] via web-mailer(MaintM3.3.0.77) on Mon Sep 27 13:34:40 GMT 1999 Date: 27 Sep 99 15:34:40 MET DST From: "Dr.Teerakiat Kerdcharoen" To: chemistry@server.ccl.net Subject: Linux distributions and FORTRAN (g77) Hi there, According to Mike Falcetta's problem on G77 compiler on Linux, I would like to share some experiences. G77 has no option to promote single precision to double precision, namely -r8, which is available in most F77 compiler. I also had disastrous results >from MD simulations without double precision. All we can do is that (1) use f2c instead (2) manually change all single precision variables to double that is laborious or (3) obtain free full function FORTRAN compiler. I suggest the WEB site, http://www.psrv.com/lnxf90.html for obtaining F90 compiler. Perhaps you need to specify some switch so as to compile F77 code. Best, Teerakiat = ____________________________________________________________________ Get free email and a permanent address at http://www.netaddress.com/?N=3D= 1 From chemistry-request@server.ccl.net Mon Sep 27 11:18:00 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 LAA27455 for ; Mon, 27 Sep 1999 11:18:00 -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 MAA17681 for ; Mon, 27 Sep 1999 12:57:13 -0400 Sender: brunob@helix.nih.gov Message-ID: <37EFA1E8.D58B396A@helix.nih.gov> Date: Mon, 27 Sep 1999 12:57:12 -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: Automatic docking with Macromodel Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id LAA27456 Hello all I am interested in automatic docking of small molecules to a protein using a program equipped with a non explicit solvent model. I plan to use the MMFF with the GB/SA water solvation model as implemented in Macromodel 6.5 for this task. I also would like selected residues of the binding site to be flexible whereas the rest of the receptor would be fixed. According to the user's manual pages 75 and 77, the MOLS option of the MC, SD and MD related commands can be used for docking searches. Unfortunately, I haven't found examples or pratical recipes to perform automatic docking this way. Could someone provide me pointers (references, recipes, examples)? I 'll summarize the answers. Thank you Bruno Bienfait -- [ 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 ] From chemistry-request@server.ccl.net Mon Sep 27 13:08:42 1999 Received: from nucleus.harvard.edu (nucleus.harvard.edu [140.247.90.196]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA28330 for ; Mon, 27 Sep 1999 13:08:42 -0400 Received: from localhost (daizadeh@localhost) by nucleus.harvard.edu (8.9.3/8.9.3) with ESMTP id NAA00742 for ; Mon, 27 Sep 1999 13:04:11 -0400 (EDT) Date: Mon, 27 Sep 1999 13:04:11 -0400 (EDT) From: Iraj Daizadeh To: CHEMISTRY@ccl.net Subject: Re: CCL:C to Fortran In-Reply-To: <37EF7312.2781@tc.cornell.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Why in the world would someone want to perform this absurd transformation? Is this a problem with the obtainment of compilers or simply a lack of programming knowledge about C/C++. [BTW; it would be impossible to convert C++ to fortran77; maybe 90 but this would take some effort.] Simply use multi-language compiling tricks which are well known to the CCL. That is, compile the fortran code, compile the C/C++ code and ligate the object files together.[There are some fine points, however--such as passing variables to functions (Since fortran always passes via `pointers' by default-thus, when you call a fortran subroutine from within C/C++ code you need to pass the variable address (&) -which can be easily introduced even in large coding projects. ] There was a post some time ago (by me) that dealt with multi-language compilation issues in a most pragmatic way--the post even contained a small tutorial-like example.] Also, if speed is what is sought-for here--optimized C is just as fast as fortran. Iraj. Iraj Daizadeh, Ph.D. Harvard University Department of Cellular and Molecular Biology The Biological Laboratories 16 Divinity Avenue Cambridge, MA 02138 Phone: (617) 495-0783 (617) 495-0560 Fax: (617) 496-4313 Email: daizadeh@nucleus.harvard.edu WebPage: http://mcb.harvard.edu/gilbert/daizadeh From chemistry-request@server.ccl.net Mon Sep 27 10:13:18 1999 Received: from pub.jlonline.com. ([202.102.24.37]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA27093 for ; Mon, 27 Sep 1999 10:13:16 -0400 Received: from chungenl ([10.74.65.25]) by pub.jlonline.com. (8.9.1/8.9.1) with SMTP id WAA21467 for ; Mon, 27 Sep 1999 22:03:52 +0800 (CST) Message-ID: <001301bf08f1$6bb7a040$19414a0a@chungenl> From: "Chungen Liu" To: Subject: Where can I found the basis sets for Ce? Date: Mon, 27 Sep 1999 22:05:56 +0800 MIME-Version: 1.0 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Hi, Every one, Is there any web sites where the basis sets of Ce can be found? Chungen From chemistry-request@server.ccl.net Mon Sep 27 12:35:11 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA27981 for ; Mon, 27 Sep 1999 12:35:11 -0400 Received: from bacchus.pc1.uni-duesseldorf.de (root@bacchus.pc1.uni-duesseldorf.de [134.99.152.11]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id MAA23424 for ; Mon, 27 Sep 1999 12:29:02 -0400 (EDT) Received: from bacchus.pc1.uni-duesseldorf.de (jochen@localhost [127.0.0.1]) by bacchus.pc1.uni-duesseldorf.de (8.8.7/8.8.7) with SMTP id SAA24463; Mon, 27 Sep 1999 18:28:28 +0200 From: Jochen Reply-To: jochen@pc1.uni-duesseldorf.de Organization: Heinrich-Heine-Universität To: Stojakovic Djordje , chemistry@www.ccl.net Subject: Re: CCL:A Linux question Date: Mon, 27 Sep 1999 18:27:46 +0200 References: <37EF5025.D37B8265@elab.tmf.bg.ac.yu> In-Reply-To: <37EF5025.D37B8265@elab.tmf.bg.ac.yu> Message-Id: <99092718282707.23454@bacchus.pc1.uni-duesseldorf.de> On Mon, 27 Sep 1999 Stojakovic Djordje wrote: >I am a chemistry student using a Pentium PC under Red Hat Linux 5.0. >Presently >I have been trying to adapt a fortran source file written for the g77 >compiler >so that it could be compiled with the f2c compiler. In doing so I have >encountered only one problem, and it refers to the g77's "loc" >statement, as in Any special reason not to use g77 on your Linux box ? -- Jochen Heinrich-Heine-Universität, Institut für Physikalische Chemie I Universitätsstr. 1, Geb. 26.43.02.29, 40225 Düsseldorf, Germany phone 02118113681 fax 02118115195 -- www-public.rz.uni-duesseldorf.de/~jochen Jochen@Uni-Duesseldorf.de -- Jochen.Kuepper@FernUni-Hagen.de -- Kuepper@ACM.org From chemistry-request@server.ccl.net Mon Sep 27 11:22:31 1999 Received: from brook.tfe.gatech.edu (brook.tfe.gatech.edu [130.207.144.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27479 for ; Mon, 27 Sep 1999 11:22:31 -0400 Received: (from hai@localhost) by brook.tfe.gatech.edu (980427.SGI.8.8.8/970903.SGI.AUTOCF) id LAA06428 for CHEMISTRY@ccl.net; Mon, 27 Sep 1999 11:12:30 -0400 (EDT) From: "Hai Dong" Message-Id: <9909271112.ZM6427@brook.tfe.gatech.edu> Date: Mon, 27 Sep 1999 11:12:30 -0400 To: CHEMISTRY@ccl.net Subject: CCL: united atom approach in InsightII Hello, Sorry, my last message is not very clear. The software I'm using is InsightII, a product of MSI. I'd like to get some help in applying united atom approach with it. Many thanks! Hai Dong hai@brook.tfe.gatech.edu From chemistry-request@server.ccl.net Mon Sep 27 11:35:34 1999 Received: from igc.phys.chem.ethz.ch (igc.ethz.ch [129.132.102.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27568 for ; Mon, 27 Sep 1999 11:35:34 -0400 Received: from igc.phys.chem.ethz.ch (sulfid.ethz.ch [129.132.126.45]) by igc.phys.chem.ethz.ch (8.8.8/8.8.8) with ESMTP id RAA29009 for ; Mon, 27 Sep 1999 17:30:11 +0200 (MET DST) Sender: nuran@igc.phys.chem.ethz.ch Message-ID: <37EF8CEA.EE827194@igc.phys.chem.ethz.ch> Date: Mon, 27 Sep 1999 17:27:39 +0200 From: Nuran Elmaci Organization: ETH To: "CHEMISTRY@server.ccl.net" Subject: mopac7, eps Dear CCL Members, I would like make some excited state calculations including solvent effects with MOPAC7, I have used EPS=n.nn and NSPA=n keywords, but the keywords are unrecognized. Is there any other keyword that I should use with them? There is a description about COSMO in the Mopac manual but the necessary keywords are not located in the keyword list. I would appreciate if someone can help me. thanks, Nuran Elmaci From chemistry-request@server.ccl.net Mon Sep 27 12:52:59 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA28159 for ; Mon, 27 Sep 1999 12:52:59 -0400 Received: from mail.chemie.fu-berlin.de (root@envelope.chemie.fu-berlin.de [160.45.24.22]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id MAA24027 for ; Mon, 27 Sep 1999 12:46:46 -0400 (EDT) Received: from Dirac.Chemie.FU-Berlin.DE (dirac.chemie.fu-berlin.de[160.45.24.166]) (2211 bytes) by mail.chemie.fu-berlin.de via sendmail with P:smtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Mon, 27 Sep 1999 18:46:27 +0200 (CEST) (Smail-3.2.0.108) Received: by Dirac.Chemie.FU-Berlin.DE (Smail3.2.0.98) id ; Mon, 27 Sep 1999 18:46:27 +0200 (MEST) Message-Id: From: melchers@chemie.fu-berlin.de (Bernd Melchers) Subject: Re: CCL:A Linux question To: stojakovic@elab.tmf.bg.ac.yu (Stojakovic Djordje) Date: Mon, 27 Sep 1999 18:46:26 +0200 (MEST) Cc: chemistry@www.ccl.net In-Reply-To: <37EF5025.D37B8265@elab.tmf.bg.ac.yu> from "Stojakovic Djordje" at Sep 27, 99 12:08:21 pm 'Stojakovic Djordje wrote:' > > Dear CClers: > > I am a chemistry student using a Pentium PC under Red Hat Linux 5.0. > Presently > I have been trying to adapt a fortran source file written for the g77 > compiler > so that it could be compiled with the f2c compiler. In doing so I have > encountered only one problem, and it refers to the g77's "loc" > statement, as in > the following program line: > > ifh=(ih-loc(fh(1)))/8+1 > NAME LOC - Obtains the address of a variable SYNOPSIS LOC ([I=]i) IMPLEMENTATION UNICOS, UNICOS/mk, IRIX systems CF90, MIPSpro 7 Fortran 90, MIPSpro Fortran 77 STANDARDS Fortran extension DESCRIPTION LOC returns the address of a variable, constant, or array. It accepts the following arguments: i The variable for which the address is being requested. Specify a variable of any data type. ... it should be possible to write a c program wrapper for this function, e.g. something like this int loc_(void *ptr) { /* assumes sizeof(int) == sizeof(void*) */ return (int)ptr; } Ciao Bernd -- Bernd Melchers | melchers@FU-Berlin.DE Freie Universitaet Berlin | "We don't write software, we compose it." AG Macromolecular Modelling - Prof. Dr. E.W. Knapp for more information see http://userpage.chemie.fu-berlin.de/~melchers/ From chemistry-request@server.ccl.net Mon Sep 27 14:10:44 1999 Received: from alpha.netaccess.on.ca (root@alpha.netaccess.on.ca [199.243.225.10]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA28844 for ; Mon, 27 Sep 1999 14:10:43 -0400 Received: from dragan (dial168.nas.net [199.243.225.168]) by alpha.netaccess.on.ca (8.9.0/8.9.0) with SMTP id OAA10357 for ; Mon, 27 Sep 1999 14:04:35 -0400 (EDT) Message-Id: <4.1.19990927140546.0099a720@mail.netaccess.on.ca> X-Sender: vuckovic@mail.netaccess.on.ca X-Mailer: QUALCOMM Windows Eudora Pro Version 4.1 Date: Mon, 27 Sep 1999 14:10:13 -0400 To: "Computational Chemistry List" From: Dragan Vuckovic Subject: EduChem - New release Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear collegues, EduChem can now perform semi-empirical calculations using EHT and PM3 methods. Many other new features. Ideal for first year general chemistry course. Check http://www.etci.on.ca. Cheers. ___________________________________ Dr. Dragan Lj. Vuckovic General Manager and CEO Exceptional Teaching Concepts, Inc. 100 George St. Suite A, Hamilton Ontario, L8P 1E2 Canada Phone:(905) 521-1579; Fax:(905) 521-2128 info@etci.on.ca; http://www.etci.on.ca From chemistry-request@server.ccl.net Mon Sep 27 15:51:49 1999 Received: from ml.wpafb.af.mil (firewall-user@ml-firewall.ml.wpafb.af.mil [134.131.90.33]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA29436 for ; Mon, 27 Sep 1999 15:51:49 -0400 Received: by ml.wpafb.af.mil; id PAA13082; Mon, 27 Sep 1999 15:45:40 -0400 (EDT) Received: from fszhtv48.ml.wpafb.af.mil(134.131.37.142) by ml-firewall.ml.wpafb.af.mil via smap (V5.0) id xma012917; Mon, 27 Sep 99 15:44:56 -0400 Received: by fszhtv48.ml.wpafb.af.mil with Internet Mail Service (5.5.2650.10) id ; Mon, 27 Sep 1999 15:43:29 -0400 Message-ID: <0163F33EE074D211810C0000F8CD23549E78F0@fszhtv48.ml.wpafb.af.mil> From: Patnaik Soumya S Contr AFRL/MLPJ To: "'chemistry@ccl.net'" Subject: call for paper Date: Mon, 27 Sep 1999 15:43:28 -0400 X-Mailer: Internet Mail Service (5.5.2650.10) Dear Colleague, I would like to bring to your attention a MRS symposium on Multiscale Modeling of Organic Materials. CALL FOR PAPERS MULTISCALE MODELING OF ORGANIC MATERIALS Materials Research Society Spring 2000 Meeting April 24-28, 2000 San Francisco, California This symposium will address accomplishments, limitations, and future directions for modeling organic materials behavior across disparate length and time scales. Some of the topics to be emphasized are: * Approaches that link atomistic & continuum modeling * Mesoscale models * Methods for producing & validating accurate potentials * Combined quantum-mechanical & atomistic approaches * Dynamical properties Symposium Organizers: Barry L. Farmer, Air Force Research Laboratory Ruth Pachter, Air Force Research Laboratory Soumya S. Patnaik, Air Force Research Laboratory David Rigby, Molecular Simulations Inc. Kohji Tashiro, Osaka University Invited Speakers Include: Y. Aoki, Hiroshima University, Japan M. Doi, Nagoya University, Japan D. Dudis, Air Force Research Laboratory B. Eichinger, Molecular Simulations Inc. J. Fraaije, University of Groningen, Netherlands S. Glotzer, National Institute of Standards & Technology W. Goddard, California Institute of Technology G. Goldbeck-Wood, Cambridge University, UK M. Gordon, Iowa State University K. Kremer, Max-Planck-Institute for Polymer Research, Germany S. Krimm, University of Michigan S. Kumar, Pennsylvania State University J. de Pablo, University of Wisconsin-Madison Y. Sasanuma, Chiba University, Japan J. Yeomans, University of Oxford, UK M. Watanabe, Moldyn, Inc. Joint sessions are anticipated with the following symposia: O: Materials Computation-Progress Towards Technological Impact S: Electrically Active Polymers CC: Hybrid Organic / Inorganic Materials DD: Interfacial Aspects of Soft Biomaterials EE: Nanostructures in Polymers Selected papers from the symposium will be published in a special issue of Computational & Theoretical Polymer Science Abstract Deadlines: October 18 - Abstracts sent via e-mail, fax or mail November 1 - Abstracts sent via the MRS Web-site For more information & instruction see the conference home page at http://www.mrs.org/meetings/spring00/cfp/symposia/p.html +++++++++++++++++++++++++++++++++++++++++++++ Soumya S. Patnaik Air Force Research Laboratory Soumya.Patnaik@afrl.af.mil AFRL/MLPJ, Bldg. 651, 3005 P St., WPAFB, OH 45433 (937) 255-6671 ext. 3116 Fax: (937) 255-1128 +++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Mon Sep 27 16:16:57 1999 Received: from ice.lanl.gov (ice.lanl.gov [128.165.22.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA29712 for ; Mon, 27 Sep 1999 16:16:56 -0400 Received: from localhost (localhost [[UNIX: localhost]]) by ice.lanl.gov (8.9.3/8.9.3) id OAA11814; Mon, 27 Sep 1999 14:10:47 -0600 From: Matt Challacombe Reply-To: MChalla@T12.LANL.Gov Organization: Group T-12, Theoretical Chemistry and Molecular Physics To: Iraj Daizadeh , CHEMISTRY@ccl.net Subject: Re: CCL:C to Fortran Date: Mon, 27 Sep 1999 14:07:48 -0600 X-Mailer: KMail [version 1.0.24] Content-Type: text/plain References: MIME-Version: 1.0 Message-Id: <9909271410470G.12903@ice.lanl.gov> Content-Transfer-Encoding: 8bit On Mon, 27 Sep 1999, Iraj Daizadeh wrote: > Why in the world would someone want to perform this absurd transformation? One reason for performing this transformation is to ensure portability for fortran-c and c-fortran interfaces where strings are passed. --Matt +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ + Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ + + Los Alamos National Laboratory email: mchalla@t12.lanl.gov + + Theoretical Division vmail: (505) 698-4112 + + Group T-12, Mail Stop B268 phone: (505) 665-5905 + + Los Alamos, New Mexico 87545 fax: (505) 665-3909 + + + + "The secret to mountain biking is pretty simple. The slower you go + + the more likely it is you'll crash." -- Julie Furtado + +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@server.ccl.net Mon Sep 27 16:23:29 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA29809 for ; Mon, 27 Sep 1999 16:23:29 -0400 Received: from ice.lanl.gov (ice.lanl.gov [128.165.22.6]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id QAA01764 for ; Mon, 27 Sep 1999 16:17:18 -0400 (EDT) Received: from localhost (localhost [[UNIX: localhost]]) by ice.lanl.gov (8.9.3/8.9.3) id OAA11855; Mon, 27 Sep 1999 14:15:18 -0600 From: Matt Challacombe Reply-To: MChalla@T12.LANL.Gov Organization: Group T-12, Theoretical Chemistry and Molecular Physics To: Stojakovic Djordje , chemistry@www.ccl.net Subject: Re: CCL:A Linux question Date: Mon, 27 Sep 1999 14:12:21 -0600 References: <37EF5025.D37B8265@elab.tmf.bg.ac.yu> Message-Id: <9909271415180H.12903@ice.lanl.gov> On Mon, 27 Sep 1999, Stojakovic Djordje wrote: > When I try to compile the source code with the f2c compiler, I get an > error > message saying "Undefined reference to 'loc_' ". > It is a simple matter to write your own loc_ (or loc or loc__) function in c: unsigned int loc_( int* a ){return (unsigned) a ;} -Matt +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ + Matt Challacombe, Ph.D. http://www.t12.lanl.gov/~mchalla/ + + Los Alamos National Laboratory email: mchalla@t12.lanl.gov + + Theoretical Division vmail: (505) 698-4112 + + Group T-12, Mail Stop B268 phone: (505) 665-5905 + + Los Alamos, New Mexico 87545 fax: (505) 665-3909 + + + + "The secret to mountain biking is pretty simple. The slower you go + + the more likely it is you'll crash." -- Julie Furtado + +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@server.ccl.net Mon Sep 27 20:44:33 1999 Received: from tele-post-20.mail.demon.net (tele-post-20.mail.demon.net [194.217.242.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA31343 for ; Mon, 27 Sep 1999 20:44:31 -0400 Received: from iainm.demon.co.uk ([158.152.30.61]) by tele-post-20.mail.demon.net with smtp (Exim 2.12 #2) id 11VlHf-000DRc-0K for chemistry@ccl.net; Tue, 28 Sep 1999 00:38:20 +0000 Message-ID: Date: Tue, 28 Sep 1999 01:37:08 +0100 To: chemistry@ccl.net From: Iain M McLay Subject: UK-QSAR Group - next meeting Oct 20th. MIME-Version: 1.0 X-Mailer: Turnpike Integrated Version 4.02 U The next meeting of the UK-QSAR and ChemoInformatics group will be on October 20th at SmithKline Beecham, Harlow in the UK. If you would like full details of the meeting please visit the meeting Web page: http://www.iainm.demon.co.uk/1999aut.htm Copies of the slides from our last meeting, which was held at Pfizer, Sandwich in the UK, are also available at http://www.iainm.demon.co.uk/1999spr.htm If you would like to know more about the group please visit the UK-QSAR and ChemoInformatics Group Web site: http://www.iainm.demon.co.uk Iain McLay e-mail:iain@iainm.demon.co.uk -- Iain M McLay From chemistry-request@server.ccl.net Mon Sep 27 16:55:04 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA30165 for ; Mon, 27 Sep 1999 16:55:01 -0400 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id QAA03512 for ; Mon, 27 Sep 1999 16:48:49 -0400 (EDT) Received: (from daemon@localhost) by bioc1.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id NAA03585; Mon, 27 Sep 1999 13:47:30 -0700 (PDT) Message-Id: <199909272047.NAA03585@bioc1.msi.com> Received: from osman-pc.msi.com(146.202.7.202) by bioc1.msi.com via smap (V2.0) id xma003565; Mon, 27 Sep 99 13:47:03 -0700 X-Sender: osman@146.202.6.217 X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Mon, 27 Sep 1999 13:48:48 -0700 To: CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, owner-qsar_society@unil.ch, chemweb@ic.ac.uk From: "Osman F. Guner" Subject: Call for Papers - Modeling and Informatics for Experimentalists 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 QAA30166 This message has been posted to: CHEMISTRY@www.ccl.net, CHMINF-L@LISTSERV.INDIANA.EDU, owner-qsar_society@unil.ch, chemweb@ic.ac.uk. Apologies for multiple-posting MODELING AND INFORMATICS FOR NON-EXPERTS To be held at the 219th National American Chemical Society Meeting in San Francisco California, March 26-30, 2000 Sponsored by the Division of Chemical Information (CINF) Computers were used to be available only to a small number of experts; today computers are a commodity. Internet were used to be accessible only by selected experts; today Internet is accessible by all. How does evolution of computational chemistry map to these paradigm changes? Informatics and modeling tools that has only been available to information scientists and computational chemists are now being used by experimental chemists, medicinal chemists. What are the consequence of this broadened use of computational tools? What are the benefits or issues? If you have an opinion on this topic, or if you know of success stories or failures in this area, you may want to consider presenting your views in this symposium. Please use the On-line Abstract System (OASys) to submit your abstracts. At http://acs.confex.com/acs/219nm/cinf/papers/index.cgi , select the symposium with the above title. The deadline for submitting abstracts is October 22, 1999. Although use of the OASys is strongly encouraged for your abstract submission, should you have difficulties with the OASys, feel free to E-mail me an electronic copy of your abstract by filling out the word template that a be downloaded at http://www.acs.org/meetings/abstract/absdown.html Cheers...Osman --- Osman F. Güner, Ph.D. Sr.Product Manager, Rational & Combinatorial Drug Design Molecular Simulations Inc. (858)799-5341 osman@msi.com http://www.msi.com From chemistry-request@server.ccl.net Mon Sep 27 16:12:58 1999 Received: from mail.wesleyan.edu (smtp.wesleyan.edu [129.133.1.61]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA29649 for ; Mon, 27 Sep 1999 16:12:58 -0400 Received: from sunfish (sunfish.chem.wesleyan.edu [129.133.20.34]) by mail.wesleyan.edu (8.9.3/8.9.1) with SMTP id QAA06778 for ; Mon, 27 Sep 1999 16:06:47 -0400 (EDT) Message-Id: <3.0.5.32.19990927160829.01282c90@wesleyan.edu> X-Sender: yliu@wesleyan.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.5 (32) Date: Mon, 27 Sep 1999 16:08:29 -0400 To: CHEMISTRY@ccl.net From: Yongxing Liu Subject: Power Mac G4, linux and bechmarking Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear CCLers, I would like to know which version of linux is optimized for Power Mac G4 processors. Does any one have built super clusters with G4? I also want to know bechmarking on G4/linux for computational chemistry programs (e.g. Charmm, Amber or g2k/g98 etc). Thanks a lot in advance! From chemistry-request@server.ccl.net Mon Sep 27 22:35:08 1999 Received: from web125.yahoomail.com (web125.yahoomail.com [205.180.60.193]) by server.ccl.net (8.8.7/8.8.7) with SMTP id WAA31822 for ; Mon, 27 Sep 1999 22:35:08 -0400 Message-ID: <19990928022923.12973.rocketmail@web125.yahoomail.com> Received: from [200.245.53.100] by web125.yahoomail.com; Mon, 27 Sep 1999 19:29:23 PDT Date: Mon, 27 Sep 1999 19:29:23 -0700 (PDT) From: Marcio Cyrillo To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi CCLers, Sometime ago I read a post from someone looking for a C to Fortran translator. Although I have many reasons to believe this kind of translation will not be successful in most of cases, I found a link to a program for Windows95/98 which is supposed to do the job: http://www.uni-comp.com/fortran/free.html My experience using f2c is that the code produced is mostly not understandable. I truly believe it is better to spend some time learning C (not C++) which is a powerful language for scientific applications. C++ seems to be worth using only if one intends to build very professional applications. Best wishes, Marcio. ===== Marcio Cyrillo - http://www.ifi.unicamp.br/~cyrillo cyrillo@ifi.unicamp.br - mcyrillo@yahoo.com - cyrillo@mail.uni-freiburg.de Graduate Student State University of Campinas - UNICAMP Campinas - SP - Brazil Applied Physics Department room 51 - phone +55 19 788 2364 __________________________________________________ Do You Yahoo!? Bid and sell for free at http://auctions.yahoo.com