From owner-chemistry@ccl.net Fri May 4 02:27:00 2007 From: "Arthit Vongachariya varthit a gmail.com" To: CCL Subject: CCL:G: Pls. Help to install Gaussian in ia64 Message-Id: <-34185-070504022343-22948-IqSNc3AXIiIPYxYhC3Jyzw(~)server.ccl.net> X-Original-From: "Arthit Vongachariya" Date: Fri, 4 May 2007 02:23:39 -0400 Sent to CCL by: "Arthit Vongachariya" [varthit*_*gmail.com] I have a problem about install gaussian03 c.02(source code) cause this platfrom (c.02) require intel compile70 (ecc and efc command) and lib mkl60 but computer that i want to install have intel_fc_80 and intel_cc_80 for compiler (icc and ifort command) and mkl70 for lib can anyone pls. tell me what file i must to edit and change PATH and how ? to be install with intel compiler80 & lib mkl70 thank you very much Arthit From owner-chemistry@ccl.net Fri May 4 03:35:00 2007 From: "Bjoern Windshuegel bjorn.windshugel]_[uku.fi" To: CCL Subject: CCL: Homology Modeling and Threading Message-Id: <-34186-070504030517-8582-SlGYGGzN40/oWCtOOtG77g-x-server.ccl.net> X-Original-From: Bjoern Windshuegel Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 4 May 2007 09:29:34 +0300 MIME-Version: 1.0 Sent to CCL by: Bjoern Windshuegel [bjorn.windshugel_+_uku.fi] Hi, Modeller is one possibility, its free of chartge for academic and non-profit institutions http://salilab.org/modeller/ Also the swiss-model might be interesting. You can use it via a web-interface http://swissmodel.expasy.org//SWISS-MODEL.html For side chain modelling I recommend SCWRL (also free for academic institutions): http://dunbrack.fccc.edu/SCWRL3.php Best regards, Bjφrn > Sent to CCL by: "Joseph E. Maxwell" [jemaxwell]*[jaymax.com] > Hello Group, > > Can someone recommend a reliable software that is reasonably priced, > Free/Shareware or Open Source for Homology Modeling and/or Threading? > > Thanks-- Dr. Bjφrn Windshόgel Department of Pharmaceutical Chemistry University of Kuopio P.O. Box 1627 70211 Kuopio, FINLAND Email: bjorn.windshugel/./uku.fi Phone: (+358) 17 162463 Fax: (+358) 17 162456 Web: www.uku.fi/farmasia/fake/modelling/index.shtml From owner-chemistry@ccl.net Fri May 4 08:26:00 2007 From: "Tim Robinson twrobinson%%manchester.ac.uk" To: CCL Subject: CCL: Parallel Programming Summer School | University of Manchester Message-Id: <-34187-070503120537-4912-zF+mptn0Jr9GjSSAdRCS/w|server.ccl.net> X-Original-From: "Tim Robinson" Date: Thu, 3 May 2007 12:05:34 -0400 Sent to CCL by: "Tim Robinson" [twrobinson ~~ manchester.ac.uk] Hi all, Our parallel programming summer school (details below) might be of interest to theoretical and computational chemistry students in the UK (and abroad). Thanks, Tim Robinson ---- Manchester Computing at the University of Manchester is pleased to announce the 2007 Parallel Programming Summer School. There are two parallel sessions: one for attendees who don't know either Fortran or C, and one for those who have experience of one of these languages. Topics for students new to programming include: . Fortran . Introduction to HPC . OpenMP . Introduction to MPI Experienced programmers will study: . Introduction to HPC . OpenMP . Introduction to MPI . Advanced MPI . Code Optimization There will also be guest lectures on broader topics in HPC. Speakers include Jack Dongarra and vendor experts. Fees, Accommodation and Meals We can provide student accommodation with private bathroom, and all meals including the Summer School night out! Registration and all other information are detailed on the web link below. Places are limited. http://www.mc.manchester.ac.uk/services/courses/summerschool From owner-chemistry@ccl.net Fri May 4 11:17:00 2007 From: "Andrew Joseph Adamczyk a-adamczyk++northwestern.edu" To: CCL Subject: CCL:G: Assigning charges for quadrupole Message-Id: <-34188-070504104225-15205-uqPF4G7JATX/Z2YUbkO+qQ[#]server.ccl.net> X-Original-From: "Andrew Joseph Adamczyk" Date: Fri, 4 May 2007 10:42:21 -0400 Sent to CCL by: "Andrew Joseph Adamczyk" [a-adamczyk(-)northwestern.edu] For calculating the quadrupole moment in diatomic nitrogen using Gaussian 03, how would I go about assigning charges (e.g., -++- or +--+ distributions). Preliminary calculations using B3LYP/6-31g* have yielded the following quadrupole results: Quadrupole moment (field-independent basis, Debye-Ang): XX= -10.0206 YY= -10.0206 ZZ= -11.5984 XY= 0.0000 XZ= 0.0000 YZ= 0.0000 Traceless Quadrupole moment (field-independent basis, Debye-Ang): XX= 0.5259 YY= 0.5259 ZZ= -1.0519 XY= 0.0000 XZ= 0.0000 YZ= 0.0000 Any comments would be greatly appreciated. Thank you. From owner-chemistry@ccl.net Fri May 4 12:03:01 2007 From: "Anselm.Horn{}chemie.uni-erlangen.de" To: CCL Subject: CCL:G: looking for free GUI for Mac Message-Id: <-34189-070504051156-19614-EsrbTOuQoObhzitdoXSUTg-x-server.ccl.net> X-Original-From: Anselm.Horn===chemie.uni-erlangen.de Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 4 May 2007 10:08:59 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Anselm.Horn_+_chemie.uni-erlangen.de Hi, > I'm looking for a free graphical interface for Mac that reads output files > from Gaussian and allows one > to easily modify the structure. I would be willing to spend some money but > certainly not close to a > mille dollars. you might be interested in "Molecule" by N.J.R. van Eikema Hommes. See http://www.chemie.uni-erlangen.de/hommes/molecule/index.html for details. Although it is not free, the licensing costs seem fair (< 300 EUR) and the terms are also very user-friendly: "[...] The license allows installation of the program on all computers belonging to the research group or institution that licensed Molecule, including installation on file-servers, and use of the program by all members of the group. In addition, group members are allowed to install the program on their private machines, e.g. for use at home. [...]" Hope that helps, Anselm From owner-chemistry@ccl.net Fri May 4 12:38:00 2007 From: "george li lgh19721031*hotmail.com" To: CCL Subject: CCL:G: Question about coding in Gaussian Message-Id: <-34190-070504114155-772-oVS5ofrK3YuyycctTn+j7A::server.ccl.net> X-Original-From: "george li" Date: Fri, 4 May 2007 11:41:51 -0400 Sent to CCL by: "george li" [lgh19721031-$-hotmail.com] Hi CCLers, I am new programmer for Gaussian(03). I am trying to use COMMON block to transfer some data between different subroutines, but when I do this, in the sender subroutine (say L101.F) it is OK, which shows all correct values for the variables, but in receiver subroutines (say L301.F) it cannot show correct values, which all of them are zero. Compilation is no problem. Could you give me some hints for how to use COMMON block in Gaussian codes? Thank you very much!!! Have a great weekend!!! From owner-chemistry@ccl.net Fri May 4 13:57:00 2007 From: "Marcel Swart marcel.swart!A!icrea.es" To: CCL Subject: CCL:G: looking for free GUI for Mac Message-Id: <-34191-070504132709-5843-VbnlrxofR0lpINGtJSnhRg%%server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=WINDOWS-1252; delsp=yes; format=flowed Date: Fri, 4 May 2007 18:56:54 +0200 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Marcel Swart [marcel.swart^-^icrea.es] Note that the Molecule program, which is indeed a very useful program, does NOT run on Intel-processor based Macs. I am still eagerly waiting for a new (native OS-X) version. On May 4, 2007, at 10:08 AM, Anselm.Horn{}chemie.uni-erlangen.de wrote: > > Sent to CCL by: Anselm.Horn_+_chemie.uni-erlangen.de > > Hi, > >> I'm looking for a free graphical interface for Mac that reads >> output files >> from Gaussian and allows one >> to easily modify the structure. I would be willing to spend some >> money but >> certainly not close to a >> mille dollars. > > you might be interested in "Molecule" by N.J.R. van Eikema Hommes. > See http://www.chemie.uni-erlangen.de/hommes/molecule/index.html > for details. > > Although it is not free, the licensing costs seem fair (< 300 EUR) > and the > terms are also very user-friendly: > "[...] The license allows installation of the program on all computers > belonging to the research group or institution that licensed Molecule, > including installation on file-servers, and use of the program by all > members of the group. In addition, group members are allowed to > install > the program on their private machines, e.g. for use at home. [...]" > > Hope that helps, > > Anselm –––––––––––––––––––––––––––––––––––––––––––– dr. Marcel Swart ICREA researcher at Institut de Quνmica Computacional Universitat de Girona Campus Montilivi 17071 Girona Catalunya (Spain) fax +34-972-418356 e-mail marcel.swart(0)icrea.es marcel.swart(0)udg.edu web http://www.icrea.es/pag.asp?id=Marcel.Swart http://iqc.udg.edu/~marcel –––––––––––––––––––––––––––––––––––––––––––– From owner-chemistry@ccl.net Fri May 4 15:24:00 2007 From: "Close, David M. CLOSED!^!mail.etsu.edu" To: CCL Subject: CCL:G: Question about coding in Gaussian Message-Id: <-34192-070504152113-8335-d3BfejHNnC1KBJy5fhjHbg[a]server.ccl.net> X-Original-From: "Close, David M." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 4 May 2007 15:20:47 -0400 MIME-Version: 1.0 Sent to CCL by: "Close, David M." [CLOSED^mail.etsu.edu] I do not know the specific answer to the problem, but I do know there are real problems with the Fortran COMMON command. It is my understanding that Gaussian uses new and old subroutines. Some of these old subroutines are from old code meant to run on 16 and 32 bit machines. So you might have to examine the word size and the Real*8 commands, etc. that set the word size. It is quite likely that you have a common block that is being used with different size words. Therefore you might have a 32 bit word somewhere that was made up of 2 16 bit words. One little mistake and you could be storing a truncated 32 bit word, and 16 bits of zeros. In the old days one could add diagnostics to the compiler print out. There were pages printed after each subroutine. Some pages were called "worksheets for variables" This was very valuable information because it showed the word size of each variable. As you say, the program compiles. Unfortunately this is the easy part. Now you have to find the subroutine that is reading a COMMON statement with the wrong size word boundaries. This is not so easy to find unless you have diagnostics. Somewhere you likely have a double precision word or array that is not being read as in double precision. Regards, Dave Close -----Original Message----- > From: owner-chemistry__ccl.net [mailto:owner-chemistry__ccl.net] Sent: Friday, May 04, 2007 11:42 AM To: Close, David M. Subject: CCL:G: Question about coding in Gaussian Sent to CCL by: "george li" [lgh19721031-$-hotmail.com] Hi CCLers, I am new programmer for Gaussian(03). I am trying to use COMMON block to transfer some data between different subroutines, but when I do this, in the sender subroutine (say L101.F) it is OK, which shows all correct values for the variables, but in receiver subroutines (say L301.F) it cannot show correct values, which all of them are zero. Compilation is no problem. Could you give me some hints for how to use COMMON block in Gaussian codes? Thank you very much!!! Have a great weekend!!!http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt