From chemistry-request@server.ccl.net Fri Oct 1 11:03:18 1999 Received: from uscmail.usc.es (uscmail.usc.es [193.144.75.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA28957 for ; Fri, 1 Oct 1999 11:03:13 -0400 Received: from qogolem (qogolem.usc.es [193.144.74.235]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id QAA15594 for ; Fri, 1 Oct 1999 16:55:49 +0200 (MET DST) From: "Armando Navarro" To: Subject: localizing virtual orbital with gamess:Summary Date: Fri, 1 Oct 1999 16:54:39 +0200 Message-ID: <01bf0c1c$e2dec0d0$eb4a90c1@qogolem.usc.es> Some time ago I posted a question about how to locailize valence and = virtual orbitals with gamess-us using the Boys method Here the response from Dr. Jensen I believe you should be able to localize any set of MOs by reading them in from a $VEC, and set ICHARG=3D-2N (N=3D# of MOs, this will make the MOs doubly occipied) and RUNTYP=3DPROP in $CONTRL. Best regards, Jan Jensen Armando Navarro Facultade de Quimica. Departamento de quimica organica Universidade de Santiago de Compostela. Spain From chemistry-request@server.ccl.net Fri Oct 1 15:08:16 1999 Received: from arthur.INS.CWRU.Edu (root@arthur.INS.CWRU.Edu [129.22.8.215]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA29969 for ; Fri, 1 Oct 1999 15:08:16 -0400 Received: from raman2.cwru.edu (chem51374.CHEM.CWRU.Edu [129.22.200.174]) by arthur.INS.CWRU.Edu with SMTP (8.8.8+cwru/CWRU-3.6) id PAA21174; Fri, 1 Oct 1999 15:01:03 -0400 (EDT) (from hxt10@po.cwru.edu for ) Message-ID: <003b01bf0c48$0911bfc0$aec81681@cwru.edu> From: "Gavin Tsai" To: Subject: isotope vibrational frequency calculations Date: Fri, 1 Oct 1999 15:03:31 -0500 Hi, This is a question at the vibration and isotope vibration calculations in G98W. The simple HCl molecule is used as an example to describe my question. Below lists the results of HCl and deturated DCl HF/6-31G** vibration calculations: HCl DCl 1 1 SG SG Frequencies -- 3179.3881 Frequencies -- 2280.2669 Red. masses -- 1.0360 Red. masses -- 2.1231 Frc consts -- 6.1702 Frc consts -- 6.5041 IR Inten -- 34.0816 IR Inten -- 17.5309 Raman Activ -- 116.6559 Raman Activ -- 60.0055 Depolar -- 0.3772 Depolar -- 0.3772 By comparing those calculation, it is very reasonable to observe the frequency of DCl is lower than HCl and the reduced masses of DCl is larger than that in HCl. The question is the force constants are different in those calculations. Theoretically, the force constants are not mass dependent. Are they mass-weighted? How does G98w calculate the reduced masses and force constants in the vibration calculations? Thanks! Gavin Tsai From chemistry-request@server.ccl.net Sat Oct 2 09:54:06 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 JAA02077 for ; Sat, 2 Oct 1999 09:54:05 -0400 Received: from aurora.nal.usda.gov (aurora.nal.usda.gov [192.54.138.38]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id JAA25845 for ; Sat, 2 Oct 1999 09:46:37 -0400 (EDT) Received: from cliff.nal.usda.gov ([192.54.138.2]) by aurora.nal.usda.gov with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2448.0) id SGQQBJ2L; Sat, 2 Oct 1999 09:46:42 -0400 Received: (from srheller@localhost) by cliff.nal.usda.gov (8.8.8+Sun/8.8.8) id JAA00957; Sat, 2 Oct 1999 09:47:32 -0400 (EDT) Date: Sat, 2 Oct 1999 09:47:32 -0400 (EDT) From: "Stephen R. Heller" To: jcicshelp , chemweb@ic.ac.uk, chminf-l@listserv.indiana.edu, orgchem@extreme.chem.rpi.edu Subject: Software for Review Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII 2 October 1999 Subject: Computer Software for Review As the Software Review Editor for the ACS Journal of Chemical Information and Computer Science (JCICS) I often get software for review in the journal. I have one (1) new software product. I am looking a person who is wlling to review this software product. In return for the review which is published in JCICS you get to keep the software or database. The review should be completed in 1-3 months. The length of the review is 4-10 double spaced typed pages. Sample reviews can be found in most of the recent issues of JCICS. Please try to give me some (short) reason to choose you over another person. I have tried this approach for about the past eight years and it is working reasonably well. (REMINDER: For those who haven't finished your reviews of software sent months and months ago, this last sentence does not apply to you!) As a result, I am continuing this new method to find reviewers using this e-mail/user group system. I reserve the right to abandon this if it is a problem, or inappropriate. I will not notify people if I have found a reviewer. If you don't hear from me within a few days I have chosen someone else to review the particular package. As I get many, many, (too many) replies to this message, please do not respond after 6 October, 1999 (Wednesday), as I am sure the software will be gone by then. I can be reached on Internet (SRHELLER@NIST.GOV). PLEASE BE SURE TO INCLUDE AN STREET ADDRESS, PHONE, and FAX NUMBER!!! (I often send the software by Federal Express.) Without this information I WILL NOT consider your request. Steve Heller The package I now have is: SCUPLT 3.0 from MDL Information Systems. It comes on a CDROM. It is a program for interactive 3D visualization and manipulation of chemical structures. Steve Heller, Guest Researcher NIST/SRD, Mail Stop: 820/113 820 Diamond Avenue, Room 101 Gaithersburg, MD 20899-2310 USA Phone: 301-975-3338 FAX: 301-926-0416 E-mail: srheller@nist.gov WWW: www.hellers.com/~steve From chemistry-request@server.ccl.net Sun Oct 3 18:40:44 1999 Received: from ns2.nycap.rr.com (root@prefetch-100bt.nycap.rr.com [24.92.33.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id SAA10082 for ; Sun, 3 Oct 1999 18:40:44 -0400 Received: from mail-atm.nycap.rr.com (root@ns3 [24.92.33.1]) by ns2.nycap.rr.com (8.9.3/8.9.3) with ESMTP id SAA19780; Sun, 3 Oct 1999 18:32:42 -0400 (EDT) Received: from claessen.nycap.rr.com (cm-24-29-72-109.nycap.rr.com [24.29.72.109]) by mail-atm.nycap.rr.com (8.9.1/8.9.1) with SMTP id SAA23706; Sun, 3 Oct 1999 18:40:01 -0400 (EDT) Reply-To: From: "Rolf Claessen" To: , "CHEMICAL INFORMATION SOURCES DISCUSSION LIST" Subject: "Top 5% Chemistry Site" September '99 Date: Sun, 3 Oct 1999 18:32:58 -0400 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3612.1700 Dear Colleagues, every month I try to find chemistry websites among the submissions that are worthwhile visiting. For September '99 the winners of the "Top 5% Chemistry Site" award are listed at http://www.claessen.net/chemistry/award_en.html Criteria are information content and design (navidation, ease of use, graphical design, look&feel, ...). Submit candidates for next month at the same URL above. Regards, Rolf Claessen ____________________ Rolf U. Claessen Email administration@claessen.net WWW http://www.claessen.net From chemistry-request@server.ccl.net Sun Oct 3 20:20:37 1999 Received: from out5.prserv.net (out5.prserv.net [165.87.194.243]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id UAA10519 for ; Sun, 3 Oct 1999 20:20:37 -0400 From: jmmckel@attglobal.net Received: from schutz (slip-32-100-232-98.ny.us.prserv.net [32.100.232.98]) by out5.prserv.net (/) with SMTP id AAA84808 for ; Mon, 4 Oct 1999 00:12:47 GMT Message-ID: <37F8FE41.7058@attglobal.net> Date: Mon, 04 Oct 1999 20:21:37 +0100 Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 3.04 (WinNT; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: FTNCHEK for NT Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit CCLer's: Under UNIX on an IBM/RS6000 I used to use FTNCHEK regularly. I have the source installed on my PC/NT, and have compiled it using MS/C++/V5. I also have CYGNUS available [lets NT think UNIX.] I need help getting the documentation generated in readable form. Has anyone dealt with this before? FTNCHEN is a great utility. Thanks! John McKelvey From chemistry-request@server.ccl.net Sun Oct 3 20:30:17 1999 Received: from web128.yahoomail.com (web128.yahoomail.com [205.180.60.197]) by server.ccl.net (8.8.7/8.8.7) with SMTP id UAA10589 for ; Sun, 3 Oct 1999 20:30:16 -0400 Message-ID: <19991004002237.19493.rocketmail@web128.yahoomail.com> Received: from [206.153.158.2] by web128.yahoomail.com; Sun, 03 Oct 1999 17:22:37 PDT Date: Sun, 3 Oct 1999 17:22:37 -0700 (PDT) From: Gustavo Mercier Reply-To: gamercier@yahoo.com Subject: amber 5.0 and pgc compilation error... To: amber@cgl.ucsf.edu, chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi! I have a linux box (Red Hat 6.0) and I am trying to compile Amber v. 5.0 using the Portland Group compilers (pgcc, pgf77). I am using a Machine.pgcc file posted as a reply in the ccl that is essentially identical to the one listed in the Amber web site. (See below.) I have applied all the patches up to bugfix.49 (although bugfixes #47 and #49 could not be applied even manually to the amber version released by Oxford, the one I own. These only apply to Leap and not the actual code that fails to compile.) I have severe compilation errors associated with some routines in the following directories: ../src/etc/rdparm ../src/carnal/etc The errors associated with the files in rdparm reflect incompatibilities between the data types returned by the function strstr() and the NULL pointer. A check of the man pages suggest that this should not be a problem. strstr() will return a NULL pointer if it fails to find a string within a target string. Questions: 1) Has anybody run into this problem and come up with a solution? I did managed to compile Amber 5.0 without patches using Machine.g77, but would like to eventually compile it using the pgf77 and MPICH since I have a dual PII box. 2) Any clues about the second error seen with the compilation of CARNAL? This may relate to the compiler since the complaint is about "main" being defined twice. Any hints would be welcomed. 3) Do the bugfixes #47 and #49 apply to the distribution of Amber v. 5.0 from Oxford? In bugfix.47 there are lines containing the string "dPolar" but I could not find these in the code. In bugfix.49 there are lines containing the strings: "elseif (dZfrom 83 to 92 in main.o /usr/local/pgi/linux86/lib/pgfmain.o: In function `main': /usr/local/pgi/linux86/lib/pgfmain.o(.text+0x4f): undefined reference to `MAIN_' Linking: make: *** [carnal] Error 1 Machine.pgcc file: ------------------------------------------------------ #! /bin/csh -f ######################################################################## # # Copyright (c) 1986, 1991, 1995 # Regents of the University of California # # All Rights Reserved # # Machine Dependency Handling System # # Bill Ross ross@cgl.ucsf.edu # An extension of work of George Seibel # # Dependencies written by various authors. # # Permission to use, copy, modify, and distribute this software and # its documentation for any purpose and without fee is hereby # granted, provided that the above copyright notice appear in all # copies and that both that copyright notice and this permission # notice appear in supporting documentation, and that the name of # the University of California not be used in advertising or # publicity pertaining to distribution of the software without # specific, written prior permission. # # THE REGENTS OF THE UNIVERSITY OF CALIFORNIA DISCLAIM ALL # WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED # WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE # UNIVERSITY OF CALIFORNIA BE LIABLE FOR ANY SPECIAL, INDIRECT OR # CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM # LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, # NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN # CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. # ######################################################################## setenv MACHINE "Linux MPI" setenv MACH F2C setenv MACHINEFLAGS " -DISTAR2 -DREGNML -DEWALD -DHAS_FTN_ERFC" # CPP is the cpp for this machine setenv CPP "/lib/cpp -traditional" # SYSDIR is the name of the system-specific source directory relative to src/*/ setenv SYSDIR Machine/f2c # COMPILER ALIASES: setenv FC "pgf77" setenv CC "pgcc" # LOADER/LINKER: setenv OPT "-O3 -Munroll -Mnoframe -tp p6 -pc 64" setenv LOAD "$FC $OPT" setenv LOADLIB "-lm" # little or no optimization: setenv L0 "$FC -c " setenv L1 "$FC -c $OPT" setenv L2 "$FC -c $OPT" setenv L3 "$FC -c $OPT" # ranlib, if it exists setenv RANLIB ranlib # spasms configuration #SPASMS MACHINE.f2c_spasms_config #SPASMS unix #SPASMS n390 #SPASMS large ------------------------------------------------- ===== -- ("`-/")_.-'"``-._ Gustavo A. Mercier,Jr.,MD,PhD (. . `) -._ )-;-,_() Hillcrest Medical Center (v_,)' _ )`-.\ ``- Dept. of Radiology _;- _,-_/ / ((,' Tulsa X-Ray Laboratory ((,.-' ((,/ 5840 South Memorial Suite 301 gamercier@yahoo.com Tulsa, OK 74145-9082 voice: 918-664-9892/fax: 918-664-6120 __________________________________________________ Do You Yahoo!? Bid and sell for free at http://auctions.yahoo.com