From chemistry-request@server.ccl.net Thu Feb 15 03:32:10 2001 Received: from aquila.cscs.ch (aquila.cscs.ch [148.187.130.150]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1F8WAw03316 for ; Thu, 15 Feb 2001 03:32:10 -0500 Received: from cscs.ch (bogno [148.187.130.109]) by aquila.cscs.ch (Mail) with ESMTP id 5E66A1A855 for ; Thu, 15 Feb 2001 09:32:17 +0100 (MET) Sender: redaelli@cscs.ch Message-ID: <3A8B940A.67A5E7DE@cscs.ch> Date: Thu, 15 Feb 2001 09:32:10 +0100 From: "Claudio Redaelli (CSCS)" Organization: Swiss Center for Scientific Computing - Via Cantonale, CH-6928 Manno (CH) X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.7 sun4u) X-Accept-Language: en, el MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: CHARMM Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCLers, Can you please send me the information about the right way to obtain the source code of the CHARMM program? I'm trying to contact the CHARMM Development Project at Harvard University both by e-mail and by fax, with no response! Thanks -- Claudio Redaelli HPC Applications Support Swiss Center for Scientific Computing From chemistry-request@server.ccl.net Thu Feb 15 04:38:04 2001 Received: from nikias.cc.uoa.gr (nikias.cc.uoa.gr [195.134.68.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1F9c2w03583 for ; Thu, 15 Feb 2001 04:38:03 -0500 Received: from localhost (jkerkin@localhost) by nikias.cc.uoa.gr (8.9.3/8.9.3) with SMTP id LAA23566; Thu, 15 Feb 2001 11:38:00 +0200 (EET) Date: Thu, 15 Feb 2001 11:38:00 +0200 (EET) From: Ioannis Kerkines To: chminf-l@listserv.indiana.edu cc: chemistry@ccl.net Subject: html2pdf? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear listmembers, I have a rather big manual in multiple HTML pages, which are "structured", in a way that there is a page for contents in the left frame with links leading on the right frame to each separate chapter. I want to print this manual, but I have to click on every link and print each frame separately. Does anybody know if there is a way to print them all together at once, or better if there exists a program that can convert these html files to pdf, postscript or a more structured format (in sequential page order)? Best Regards John From chemistry-request@server.ccl.net Thu Feb 15 04:15:44 2001 Received: from relay.unizar.es (aspe.unizar.es [155.210.3.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1F9Fhw03546 for ; Thu, 15 Feb 2001 04:15:43 -0500 Received: from posta.unizar.es (posta.unizar.es [155.210.11.16]) by relay.unizar.es (8.11.1/8.11.1) with ESMTP id f1F9FKv07383 for ; Thu, 15 Feb 2001 10:15:20 +0100 (MET) Received: from qo_ttf-p3 ([155.210.88.182]) by posta.unizar.es (8.9.1/8.9.1) with SMTP id KAA11400 for ; Thu, 15 Feb 2001 10:13:56 +0100 (MET) Message-ID: <002001c0972f$e4a9bc40$b658d29b@qo_ttf-p3> From: "Jesus Orduna" To: "CCL" Subject: G98w and Athlon Date: Thu, 15 Feb 2001 10:15:51 +0100 Hi all, We are planning the purchase of a new computer to run our calculations = using the windows version of Gaussian 98. Up to date we have been using Intel pentium III based machines but now = we want to know of anybody having experience running this software on = athlon computers. Does it run properly?. How good is the performance of = this system compared to Pentium III computers? Regards, Jesus Orduna Instituto de Ciencia de Materiales de Aragon Unidad de Nuevos Materiales Org=E1nicos Facultad de Ciencias CSIC-Universidad de Zaragoza E-50009 Zaragoza (Spain) Phone/FAX: +34 976 761194 e-mail: jorduna@posta.unizar.es From chemistry-request@server.ccl.net Thu Feb 15 10:56:22 2001 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1FFuLw05356 for ; Thu, 15 Feb 2001 10:56:21 -0500 Received: from mail.chem.tamu.edu ([165.91.177.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Thu, 15 Feb 2001 10:07:50 -0600 Sender: yubo@ccl.net Message-ID: <3A8BA80F.B01795EF@mail.chem.tamu.edu> Date: Thu, 15 Feb 2001 09:57:36 +0000 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: G98 cannot use more memory Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone, I have got a new account on a SGI workstation to run G98 jobs. The problem is I cannot to allocate memory more than 48MB to the jobs. If I set more, the jobs will stop immediately after Link1. I don't why and how to solve it. Any advice? Thanks in advance Yubo -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ From chemistry-request@server.ccl.net Thu Feb 15 11:38:00 2001 Received: from avocet.prod.itd.earthlink.net (avocet.prod.itd.earthlink.net [207.217.121.50]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1FGc0w05694 for ; Thu, 15 Feb 2001 11:38:00 -0500 Received: from quantum (ip143.dayton11.oh.pub-ip.psi.net [38.31.203.143]) by avocet.prod.itd.earthlink.net (EL-8_9_3_3/8.9.3) with ESMTP id IAA15446 for ; Thu, 15 Feb 2001 08:37:54 -0800 (PST) Message-ID: <00b201c0976e$0f53c9c0$0300a8c0@quantum> Reply-To: "Kevin Gross" From: "Kevin Gross" To: "CCL" Subject: DFT and Koopmans' theorem Date: Thu, 15 Feb 2001 11:40:47 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi all, Does Koopmans' theorem still hold for MO energies obtained from DFT calculations? I'm curious because I've found that HOMO & LUMO energies obtained from HF calculations are much better regression descriptors than are the energies taken from identical B3LYP calcs. Any comments or references regarding this topic will be summarized. Thanks, Kevin Gross From chemistry-request@server.ccl.net Thu Feb 15 11:38:16 2001 Received: from mail.iinet.net.au ([203.59.24.17]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f1FGcEw05705 for ; Thu, 15 Feb 2001 11:38:14 -0500 Received: (qmail 3653 invoked by uid 666); 15 Feb 2001 16:37:53 -0000 Received: from unknown (HELO pythagoras) (203.59.177.51) by mail.iinet.net.au with SMTP; 15 Feb 2001 16:37:53 -0000 Message-Id: <4.2.2.20010216002609.00a73b10@mail.iinet.net.au> X-Sender: NONE@junk (Unverified) X-Mailer: QUALCOMM Windows Eudora Pro Version 4.2.2 Date: Fri, 16 Feb 2001 00:40:42 +0800 To: Ioannis Kerkines From: "Vincent A. Patrick" Subject: Re: CCL:html2pdf? Cc: chemistry@ccl.net In-Reply-To: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hello, You might want to try the programme "Htmldoc", which is free (Gnu licence) and available for Unix or Windows at http://www.easysw.com/htmldoc/. Cheers, Vincent Patrick ----------------------------------------------------------------------------- At 11:38 15/02/2001 +0200, Ioannis Kerkines wrote: >Dear listmembers, > >I have a rather big manual in multiple HTML pages, which are "structured", >in a way that there is a page for contents in the left frame with links >leading on the right frame to each separate chapter. > >I want to print this manual, but I have to click on every link and print >each frame separately. Does anybody know if there is a way to print them >all together at once, or better if there exists a program that can convert >these html files to pdf, postscript or a more structured format (in >sequential page order)? > >Best Regards >John ------------------------------------- From chemistry-request@server.ccl.net Thu Feb 15 17:06:05 2001 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1FM65w07052 for ; Thu, 15 Feb 2001 17:06:05 -0500 Received: from cornell.edu (carbo2.foodsci.cornell.edu [132.236.147.61]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id RAA06452; Thu, 15 Feb 2001 17:06:06 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3A8C5113.6B59E24A@cornell.edu> Date: Thu, 15 Feb 2001 16:58:43 -0500 From: "Dr. Richard Wood" Organization: Cornell University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: I'm confused about CHARMM Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I'm still confused about this hydrogen bond thing. I can use the COOR DIST cut command in the following way: set 1 1 LABEL LOOP TRAJ READ COOR DIST cut 3.0 sele segid WAT .and. type H* end - sele segid CBHL .and. type O* end COOR DIST cut 3.0 sele segid WAT .and. type H* end - sele segid CBHL .and. type N* end COOR DIST cut 3.0 sele segid WAT .and. type H* end - sele segid MANN .and. type O* end COOR DIST cut 3.0 sele segid WAT .and. type OH2 end - sele segid CBHL .and. type H* end COOR DIST cut 3.0 sele segid WAT .and. type OH2 end - sele segid MANN .and. type H* end COOR DIST cut 3.0 sele segid WAT .and. type OH2 end - sele segid WAT .and. type H* end COOR DIST cut 3.0 sele segid MANN .and. type O* end - sele segid MANN .and. type H* end increment 1 by 1 IF 1 LE @NTOT GOTO LOOP to get lists of pairs of "hydrogen bonded" atoms from each 1 ps set of a trajectory. The last two statements involve waters and sugars and include pairs that are in the same molecule and I don't know how to make it so that they aren't counted. In other words, the oxygen and hydrogen of an OH group of a sugar, for example, shouldn't be i ncluded because they are bonded to each other. The thing is, how do I know that any pair of atoms A---H are a true hydrogen bond from this type of "calculation"? I know that there is an HBONDS command that one can use in DYNAMICS; does one have to do this in order to get H-bond information? If I try and put a PRINT HBONDS command in an input file, I get a message that says certain atoms don't have h-bond parameters, in other words the parameters are missing. Then supposedly there is COOR HBOND, but I don't know a lot about that either. Still confused about CHARMM Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Thu Feb 15 18:26:52 2001 Received: from chemie.fu-berlin.de (bohr.chemie.fu-berlin.de [160.45.24.161]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1FNQqw07358 for ; Thu, 15 Feb 2001 18:26:52 -0500 Received: from localhost (winkelma@localhost) by chemie.fu-berlin.de (8.10.2/8.9.3) with ESMTP id f1FNQog05439; Fri, 16 Feb 2001 00:26:50 +0100 Date: Fri, 16 Feb 2001 00:26:50 +0100 (CET) From: Daniel Winkelmann To: Ioannis Kerkines cc: chminf-l@listserv.indiana.edu, chemistry@ccl.net Subject: Re: CCL:html2pdf? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, On Thu, 15 Feb 2001, Ioannis Kerkines wrote: > I want to print this manual, but I have to click on every link and print > each frame separately. Does anybody know if there is a way to print them > all together at once, or better if there exists a program that can convert > these html files to pdf, postscript or a more structured format (in > sequential page order)? Have a look at : http://www.easysw.com/htmldoc/ Hope that helps. Daniel Winkelmann +------------------------------------------------------------------+ | Daniel Winkelmann | | AG Knapp, Institut fuer Kristallographie | | Freie Universitaet Berlin Tel. : +49 30 838-53890 | | Takustrasse 6 Fax. : +49 30 838-53464 | | D-14195 Berlin Email : winkelma@chemie.fu-berlin.de | +------------------------------------------------------------------+