From chemistry-request@server.ccl.net Mon Jun 18 15:20:07 2001 Received: from narnia4.rutgers.edu ([165.230.180.169]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5IJK6502937 for ; Mon, 18 Jun 2001 15:20:06 -0400 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by narnia4.rutgers.edu (8.8.8/8.8.8) with ESMTP id PAA23968 for ; Mon, 18 Jun 2001 15:20:07 -0400 (EDT) Message-ID: <3B2E55E1.11C7DDB3@eden.rutgers.edu> Date: Mon, 18 Jun 2001 15:26:25 -0400 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: calculation of Ka Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers: Can anyone tell me the best way to calculate the Ka's for molecules using the thermodynamic data from the Gaussian program? Thank-you. Mary O'Connor Doctoral Candidate Rutgers University New Brunswick,NJ 08903 From chemistry-request@server.ccl.net Mon Jun 18 09:44:19 2001 Received: from cio-qmail1.mycio.com ([64.75.31.67]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5IDiH529556 for ; Mon, 18 Jun 2001 09:44:17 -0400 Received: (qmail 2096 invoked from network); 18 Jun 2001 13:43:37 -0000 Received: from cio-vscrn2.mycio.com (64.75.31.84) by cio-qmail1.mycio.com with SMTP; 18 Jun 2001 13:43:37 -0000 Received: from advsyntech.com (216.215.210.5) by cio-vscrn2.mycio.com (64.75.31.84), id <992871826256.13943820.cio-vscrn2.mycio.com>; Mon, 18 Jun 2001 06:43:46 -0700 Received: from advsyntech.com ([192.168.0.5]) by advsyntech.com (8.10.2/8.10.2/SuSE Linux 8.10.0-0.3) with ESMTP id f5IDiOP07436; Mon, 18 Jun 2001 09:44:24 -0400 X-Authentication-Warning: meridian.advsyntech.com: Host [192.168.0.5] claimed to be advsyntech.com Sender: m.frierson@advsyntech.com Message-ID: <3B2E05A6.2B615B3D@advsyntech.com> Date: Mon, 18 Jun 2001 09:44:07 -0400 From: "Dr. Manton R. Frierson" Organization: Advanced SynTech X-Mailer: Mozilla 4.7 [en] (X11; U; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net CC: Martin Gillis Subject: Re: CCL:sgi office apps??? References: <3B293617.D1BBC3BD@scripps.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit There is also a commercial product called Applix Office that I believe is still avaliable for the SGI (as well as other platforms: Unix, Linux, NT, etc.) which is comparable in function to the Word Office Suite. I have been a user of it now for several years. See http://www.vistasource.com ...... Christoph Weber wrote: > Alain Borel wrote: > > > > On 14-Jun-01 Martin Gillis wrote: > > > Hi all, > > > > > > I am curious if anyone knows of an office package for a sgi machine. > > > Apps, such as, doc. processing, spreadsheets, etc.... > > > > Maybe you can find IRIX binaries of StarOffice or OpenOffice? > > http://www.openoffice.org > > > > Otherwise: AbiWord, Gnumeric (from the Gnome project http://www.gnome.org). > > And of course, unbeatable for document preparation: LaTeX > > There's a GUI on top of LaTeX, Lyx, which makes working with LaTeX far > easier for the novice and lets one concentrate on creating content > rather than wrestle with software or text formatting. > LaTeX and Lyx are available on SGI's freeware CD and web site. > -- ####################################### # Manton R. Frierson, Ph.D. # # Computational Chemistry # # and Informatics # # Advanced SynTech # # 9800 Bluegrass Parkway # # Louisville, KY 40299 USA # # e-mail: m.frierson@advsyntech.com # # FAX: (561)258-5783 # # Ph. (502)499-0122 X107 # ####################################### From chemistry-request@server.ccl.net Mon Jun 18 16:32:58 2001 Received: from sage.plu.edu ([152.117.1.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5IKWs504041 for ; Mon, 18 Jun 2001 16:32:55 -0400 Received: from plu.edu (catbert.chem.plu.edu [152.117.8.188]) by alias.plu.edu (PMDF V5.2-31 #46615) with ESMTP id <0GF500C6F7QU9Q@alias.plu.edu> for chemistry@ccl.net; Mon, 18 Jun 2001 13:32:54 -0700 (PDT) Date: Mon, 18 Jun 2001 13:37:24 -0700 From: "Kristy L. Mardis" Subject: Vega V1.2 on Linux To: CCL Message-id: <3B2E6683.9B0C7D4E@plu.edu> Organization: Chemistry Department MIME-version: 1.0 X-Mailer: Mozilla 4.77 [en] (Windows NT 5.0; U) Content-type: MULTIPART/MIXED; BOUNDARY="Boundary_(ID_kckAbZsnHB24YCamjcmdwg)" X-Accept-Language: en This is a multi-part message in MIME format. --Boundary_(ID_kckAbZsnHB24YCamjcmdwg) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Has anyone compiled Vega 1.2 on a Linux machine (Redhat 7.0) using gcc or cc? The executable I downloaded works, but I need to make some changes to the source code and recompile. Unfortunately, even without any changes, the compilations fails with the following error message: In file included from ../pk_z.c:17: ../Z32/Z32.h:44: parse error before `char_type' ../Z32/Z32.h:44: warning: data definition has no type or storage class ../Z32/Z32.h:62: parse error before `u_short' ../Z32/Z32.h:62: warning: no semicolon at end of struct or union ../Z32/Z32.h:79: parse error before `zs_buf' ../Z32/Z32.h:79: warning: data definition has no type or storage class ../Z32/Z32.h:88: parse error before `char_type' ../Z32/Z32.h:88: warning: no semicolon at end of struct or union ../Z32/Z32.h:88: warning: no semicolon at end of struct or union ../Z32/Z32.h:92: parse error before `zs_gbuf' ../Z32/Z32.h:92: warning: data definition has no type or storage class ../Z32/Z32.h:93: parse error before `}' ../Z32/Z32.h:93: warning: data definition has no type or storage class ../Z32/Z32.h:94: parse error before `}' ../Z32/Z32.h:94: warning: data definition has no type or storage class ../Z32/Z32.h:95: parse error before `}' ../Z32/Z32.h:95: warning: data definition has no type or storage class ../Z32/Z32.h:104: parse error before `*' ../Z32/Z32.h:111: parse error before `*' ../Z32/Z32.h:119: parse error before `*' ../Z32/Z32.h:119: warning: data definition has no type or storage class ../Z32/Z32.h:126: parse error before `*' ../Z32/Z32.h:133: parse error before `*' ../pk_z.c:32: parse error before `*' ../pk_z.c: In function `Z_DepackFile': ../pk_z.c:43: `FI' undeclared (first use in this function) ../pk_z.c:43: (Each undeclared identifier is reported only once ../pk_z.c:43: for each function it appears in.) ../pk_z.c:45: parse error before `short' ../pk_z.c:50: `Ret' undeclared (first use in this function) make: *** [pk_z.o] Error 1 If anyone has already worked this problem out, I'd appreciate any help you might offer. Thanks, Kristy L. Mardis Pacific Lutheran University --Boundary_(ID_kckAbZsnHB24YCamjcmdwg) Content-type: text/x-vcard; name=mardiskl.vcf; charset=us-ascii Content-description: Card for Kristy L. Mardis Content-disposition: attachment; filename=mardiskl.vcf Content-transfer-encoding: 7BIT begin:vcard n:Mardis;Kristy L. tel;work:(253) 535-7554 x-mozilla-html:FALSE org:Pacific Lutheran University;Chemistry adr:;;241 Rieke;Tacoma;WA;; version:2.1 email;internet:mardiskl@plu.edu title:Assistant Professor fn:Kristy L. Mardis end:vcard --Boundary_(ID_kckAbZsnHB24YCamjcmdwg)-- From chemistry-request@server.ccl.net Mon Jun 18 16:02:23 2001 Received: from physics.lsu.edu ([130.39.182.96]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5IK2N503524 for ; Mon, 18 Jun 2001 16:02:23 -0400 Received: from localhost (vani@localhost) by physics.lsu.edu (8.9.2/8.9.2) with ESMTP id OAA02495 for ; Mon, 18 Jun 2001 14:55:16 -0500 (CDT) Date: Mon, 18 Jun 2001 14:55:16 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, while simulating water, i used the parameters from the TIP3 model( ref:Jorgensen et al. J.chem.Phys vol.79,1983). I had no problem. But since i have an interest in simulating biological systems in water, i used the AMBER parameters for water, but had some pathological problems. The LJ repulsion parameters between oxygen-oxygen 'seems' to be unable to counter the huge attraction between hydrogen and oxygen( of two different water molecules). Why is that so?.. in other words why were the parameters for the Lennard-Jones potential changed in AMBER? Can i use TIP3 water parameters and for protiens AMBER parameters? or..is it essential to use AMBER parameters for both proteins and water? PS: Iam not using AMBER code. Thanks vani From chemistry-request@server.ccl.net Mon Jun 18 04:47:23 2001 Received: from web12307.mail.yahoo.com ([216.136.173.105]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f5I8lM520671 for ; Mon, 18 Jun 2001 04:47:22 -0400 Message-ID: <20010618084722.79138.qmail@web12307.mail.yahoo.com> Received: from [62.90.24.187] by web12307.mail.yahoo.com; Mon, 18 Jun 2001 01:47:22 PDT Date: Mon, 18 Jun 2001 01:47:22 -0700 (PDT) From: omar Deeb Subject: joint project To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear sir, I am Dr. Omar Deeb , the chairman of the department of chemistry and chemical technology at Alquds University in Jerusalem. I finished my PhD in computational chemistry from the Hebrew university in Jerusalem and it was under the supervision of prof. Goldblum in 1993 and then i did a postdoctoral study in France in the university of Orleans under the supervision of prof Chretien. These studies concentrate on the different conformations of some analgesics such as morphine and others as well as building models of the m-receptor. I am know searching for someone in computational chemistry in which we can do a joint project or visit his or her lab to continue in this field. I will will give more information later on if necessary. THank you Dr. Omar Deeb Chairman of the department of chemistry faculty of science and technology Alquds University Jerusalem E-mail deeb2000il@yahoo.com fax 972-2-2796960 __________________________________________________ Do You Yahoo!? Spot the hottest trends in music, movies, and more. http://buzz.yahoo.com/ From chemistry-request@server.ccl.net Mon Jun 18 02:44:39 2001 Received: from mail.zrz.tu-berlin.de ([130.149.4.15]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f5I6id511863 for ; Mon, 18 Jun 2001 02:44:39 -0400 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail.zrz.tu-berlin.de with esmtp (exim-3.22) for id 15Bsm3-0000b6-00; Mon, 18 Jun 2001 08:44:35 +0200 Received: from natrium.chem.tu-berlin.de ([130.149.42.210]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.22) for id 15Bsm2-0002uj-00; Mon, 18 Jun 2001 08:44:34 +0200 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: Date: Mon, 18 Jun 2001 08:44:30 +0200 To: chemistry@ccl.net From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: G98 i386 Makefile Content-Type: text/plain; charset="us-ascii" ; format="flowed" I just saw a new "i386" Makefile from D.Fox which was meant to solve some linker problems. However, the bug is not fixed, and I consider this Makefile a very dangerous one (depending on the linker version, the block data unit might not be linked). It is clear for a stable "make" for e.g. l402.exe, you need to perform three steps: (1) copy l402.a to s save place (2) extract AND DELETE the block data (bd0402.o) (3) do the link -- no problem now, since bd0402.o no longer resides in l402.a (4) restore the original l402.a e.g.: l402.exe: $(EXTRAS) l402.a $(RUNFSP) -e m$* $(BSDDIR)/main.F $(RUNMAKE) $(MAKELOC) OPTFLAG='$(OPTFLAG)' $(EXTRAS) $*.a m$*.o !!!! cp l402.a l402_save_place.a ar x l402.a bd0402.o !!!! ar d l402.a bd0402.o $(RUNF77) $(FFLAGS) -o $*.exe m$*.o $(EXTOBJ) $*.a bd0402.o $(EXTRAS) $(GAULIB) $(LIBS) rm -f m$*.* bd0402.o !!!! mv l402_save_place.a l402.a (lines with !!!! were added). This fix is so obvious that I do not know why Gaussian still has not solved the problem. This must also be applied to the other links with block-data units. I hope that this message makes it into the archives to get rid of this infamous link problem once for all.