From owner-chemistry@ccl.net Tue May 8 04:01:01 2007 From: "syed Tarique Moin tarisyed+*+yahoo.com" To: CCL Subject: CCL: Floating Point Exception Message-Id: <-34209-070508015627-29082-RyhGKDb5O7QGC/0mkpNvdw=-=server.ccl.net> X-Original-From: "syed Tarique Moin" Date: Tue, 8 May 2007 01:56:22 -0400 Sent to CCL by: "syed Tarique Moin" [tarisyed^^yahoo.com] Hello, I updated the my linux platform but i got that when run the gaussview program, it is giving the floating point exception error. I want assistance in this regard. Regards Tarique From owner-chemistry@ccl.net Tue May 8 07:33:00 2007 From: "Toomas Tamm tt-ccl2(_)kky.ttu.ee" To: CCL Subject: CCL:G: Question about coding in Gaussian Message-Id: <-34210-070507043843-2311-LcGpFIc45uGYSkfShCiqtw#,#server.ccl.net> X-Original-From: Toomas Tamm Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 7 May 2007 10:38:38 +0300 Mime-Version: 1.0 Sent to CCL by: Toomas Tamm [tt-ccl2^_^kky.ttu.ee] Given the diversity of replies to this question, I wish to express support to the view of Ödön Farkas, which in my opinion best agrees with the symptoms descibed in the original question. L101 and L301 are different executables. All data values are lost once L101 terminates, and initialized to zero when L301 starts. If data needs to be transfered from L101 to L301, it must be written to a disk file in L101 and read back in L301. I do not know how easy or difficult it is to add one's own COMMON block to the list of blocks which need to be written to the read-write file and retrieved in the other link, but this seems to be the way to go. Alternatively, the programmer might write data to a file he creates just for this purpose and then read it back. The latter may be easier to implement for ad-hoc experiments but may create problems (eg with portability) if the code is expected to be used by others, in other environments, etc. -- Toomas Tamm e-mail: tt-ccl2 (at) kky . ttu . ee Chair of Inorganic Chemistry voice: INT+372-620-2810 Tallinn University of Technology fax: INT+372-620-2828 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ On Sat, May 05, 2007 at 05:32:06PM +0200, Ödön Farkas farkas%%chem.elte.hu wrote: > > Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas++chem.elte.hu] > Hi, > > It seems to be a simple problem. If you want using a COMMON block to > transfer data between different executables, you have to make sure it is > written out to the read-write file and then in the other program it is > read and the COMMON block is initialized. > > Best wishes, > > Ödön > > On Fri, 2007-05-04 at 11:41 -0400, george li lgh19721031*hotmail.com > wrote: > > 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!!!> > > > > > -- > Ödön Farkas > Associate professor > Deparment of Organic Chemistry and > Laboratory of Chemical Informatics, > Institute of Chemistry, > Eötvös Loránd University, Budapest > Address: 1/A Pázmány Péter sétány, > H-1117 Budapest, Hungary > Phone: +36-1-372-2570 > Cell phone: +36-30-255-3111 > Fax: +36-1-372-2620 > URL: http://organ.elte.hu/farkas> > From owner-chemistry@ccl.net Tue May 8 08:53:01 2007 From: "soumya s soumya_samineni a rediffmail.com" To: CCL Subject: CCL: Surface Coverage Calculations Message-Id: <-34211-070508085136-25369-y+gCr+eSyyz9uA+o1zoVZA%%server.ccl.net> X-Original-From: "soumya s" Date: Tue, 8 May 2007 08:51:33 -0400 Sent to CCL by: "soumya s" [soumya_samineni|a|rediffmail.com] I have generated Al(111) 3X3 surface with slab depth of 4 layers. Can you please suggest me how can i now generate monolayers of additional atoms (like Si) with different surface overages ..? 0.25ML, 0.5 ML and 1 ML . thanx in advace soumya From owner-chemistry@ccl.net Tue May 8 10:07:00 2007 From: "Kalyan chaitanya kalyanpulipaka _ gmail.com" To: CCL Subject: CCL: query regarding Zdock/Rdock Message-Id: <-34212-070508090619-475-/rJwuiT2qHQsfhrt6tZFCQ(_)server.ccl.net> X-Original-From: "Kalyan chaitanya" Content-Type: multipart/alternative; boundary="----=_Part_53646_9664781.1178625915424" Date: Tue, 8 May 2007 17:35:15 +0530 MIME-Version: 1.0 Sent to CCL by: "Kalyan chaitanya" [kalyanpulipaka]*[gmail.com] ------=_Part_53646_9664781.1178625915424 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all i have recently started protein-protein docking and likely to get started with Zdock/Rdock, but iam facing a challenge regarding the installation of the same software, is there any one who is working on this and help me.... Thankyou in advance, Regards, P.Kalyan ------=_Part_53646_9664781.1178625915424 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all

i have recently started protein-protein docking and likely to get started with Zdock/Rdock, but iam facing a challenge regarding the installation of the same software, is there any one who is working on this and help me....

Thankyou in advance,

Regards,

P.Kalyan
------=_Part_53646_9664781.1178625915424-- From owner-chemistry@ccl.net Tue May 8 10:42:00 2007 From: "Markus Doerr MarkusDoerr(-)gmx.de" To: CCL Subject: CCL:G: molden format: norm of orbitals Message-Id: <-34213-070508102905-2969-mDuARxOM/hGAxZK2BlgRJg^^^server.ccl.net> X-Original-From: "Markus Doerr" Date: Tue, 8 May 2007 10:29:02 -0400 Sent to CCL by: "Markus Doerr" [MarkusDoerr===gmx.de] Hello everybody, maybe there is someone out there who has more experience with molden files and who can help me. I have written a small tool which generates cube files from a molden file that was generated by tm2molden from a turbomole calculation (I am planning to calculate densities and differential densities using natural orbital occupations from a program that builds upon the turbomole calculation and uses turbomole's MOs). The problem is that my calculated density (and also my calculated molecular orbitals) are not normalized correctly. The shape of the orbitals in my cube file looks similar to the shape of the MOs generated directly from the molden file using molden, but my orbitals are more compact (and their calculated norm is too small). My question: Is there anything special about the norm of the MOs in the molden file that I forgot to consider when calculating the MOs? Details of my approach below. Any help would be highly appreciated. Markus Details: The molden files I am using contain cartesian gaussian primitives. I take the exponents and contraction coefficients of the primitives from the GTO section in the molden file. When summing up the primitives to form a contracted STO I include the usual normalization factors for each cartesian gaussian (setting these factors to 1 did not solve the problem). The MOs are then calculated by summing up all the STOs multiplied with the coefficients from the MO section. To check the norm of the orbital I sum up all the MO^2 * dxdydz in my cube file. Playing around with the resolution and the dimensions of the cube did not solve the problem. Of course there may be a bug somewhere else in my program, but I already spent quite a lot of time checking the code (and correcting some bugs), but now I do not find any further bug, so I thought that maybe there is a different problem. From owner-chemistry@ccl.net Tue May 8 15:45:00 2007 From: "Andreas Bender andreas.bender^complife.org" To: CCL Subject: CCL: CompLife'07: Life Science Free Software Session-Call for Contributions Message-Id: <-34214-070508154313-10858-aNtca1aanmyfriURJUlwgA(0)server.ccl.net> X-Original-From: "Andreas Bender" Date: Tue, 8 May 2007 15:43:09 -0400 Sent to CCL by: "Andreas Bender" [andreas.bender*_*complife.org] Hi All, A lot of free software exists in the Life Sciences which we are not aware of. We are currently organizing a conference focusing on Computational Life Sciences, and during this conference we are also planning to include Free Software Tutorials as well as a Free Software Session. At the last (second) CompLife conference in Cambridge (England) we had about 15 people presenting their toolkits, from the Chemistry Development Kit (CDK) over KNIME (a pipelining tool in the spirit of PipelinePilot) to Systems Biology tools such as Cytoscape. (See http://www.inf.uni-konstanz.de/complife06/freesoft.html for more information about last year's session.) So if *you* are also developing free software in the chemical or biological sciences and would like to get known with it - just read below! You are cordially invited to join us in Utrecht at the Free Software Session of this year's CompLife conference. Best wishes and hope to see you in the Netherlands! Andreas ====================================================================== Call for Proposals and Contributions for LIFE SCIENCE FREE SOFTWARE TUTORIALS and the LIFE SCIENCE FREE SOFTWARE SESSION to be held at CompLife 2007 ( http://www.complife.org/ ) in Utrecht, The Netherlands, on October 3-6, 2007 ====================================================================== ====================================================================== LIFE SCIENCE FREE SOFTWARE SESSION held at CompLife 2007 (http://www.complife.org/) in Utrecht, The Netherlands, on October 4-6, 2007 ====================================================================== In recent years more and more free and open-source software has been developed for chemo- and bioinformatics, molecular modeling or other Life Science applications, however, many of the programs are not well known. Following the great success of last year's Free Software Session at CompLife 2006 we are organizing another special session dedicated to this type of free software. Authors of free software will have the opportunity to present their program to the CompLife audience during the welcome reception which will consist of researchers and users from computer science, biology, chemistry and everything in between. In case you are interested in the free software session, send us an email to fss]-[complife.org and briefly describe your program and how you intend to present it at the conference (1-2 pages max - please include URL to downloadable version where available). The only restrictions are that the program be freely available or even open source; it must also be related to Life Science applications. The deadline for these proposals is June 22, 2007. In mid-July we will notify you if your software demo has been accepted. ====================================================================== LIFE SCIENCE FREE SOFTWARE TUTORIALS held at CompLife 2007 ( http://www.complife.org/ ) in Utrecht, The Netherlands, on October 3, 2007 ====================================================================== The CompLife organizing committee invites proposals for tutorials to be held in conjunction with the conference. Although a variety of free software programs, libraries or public datasources are available in the area of Life Sciences, many researchers do not know they exist or are afraid of using because of their apparent complexity. For this reason, we are seeking proposals for tutorials that teach interested researchers and users how to use such libraries, programs, public databases, etc. The tutorials are intended to last about 1.5 to 2 hours and will be held the day before the main conference. IMPORTANT DATES: Tutorial proposals due: June 1, 2007 Notification of acceptance/rejection: July 1, 2007 Tutorial matrial due: September 16, 2007 PROPOSAL DETAILS: Proposals should be submitted electronically by June 1 to the tutorial chairs tutorials]-[complife.org. Proposals should be in either PDF or ASCII format and include the following: * Basic information: Title, brief description, name and contact information for each tutor, length of the proposed tutorial. * Audience: Proposals must clearly identify the intended audience for the tutorial (e.g., end-users, programmers, researchers). What background will be required of the audience? Why is this topic important/interesting to the community? What is the benefit to participants? * Coverage: Enough material should be included to provide a sense of both the scope of material to be covered and the depth to which it will be covered. The more details that can be provided, the better. * Bios: Brief biographical information on each tutor (including qualifications with respect to the tutorial's topic). * Special Equipment: Please indicate any additional equipment needed (if any). The standard equipment includes a LCD projector, a single projection screen and microphones. We look forward to receiving your contributions. -- Computational Life Sciences '07 Utrecht/The Netherlands, 4-6 October 2007 Visit http://www.complife.org ! Andreas Bender, Novartis, Cambridge/MA - http://www.andreasbender.de From owner-chemistry@ccl.net Tue May 8 16:20:00 2007 From: "Markus Doerr markusdoerr**gmx.de" To: CCL Subject: CCL: molden format: norm of orbitals Message-Id: <-34215-070508155156-13960-Mg8pfjGiQCzjNpv+Rkdt/g###server.ccl.net> X-Original-From: "Markus Doerr" Date: Tue, 8 May 2007 15:51:51 -0400 Sent to CCL by: "Markus Doerr" [markusdoerr _ gmx.de] (My normal reply email was rejected, so I use the web form) Maciej Haranczyk wrote: > Dear Markus, > > It might be kind of obvious, but are your sure your cubes are large > enought ? > > Recently I had similar problem. The integrated density for 1 electron > sum up to 0.8-0.85. Obviously the remaining 0.15-0.2 of electron was > outside of the cube since it was described by very > diffuse wavefunction. > > Regards, > Maciek > Hello Maciek, thanks for the reply. However, this does not solve the problem. My first thought also was that the cube size or the resolution was too small, but I played around with the cube size and also with the resolution (the number of data points in the cube) without getting the correct norm of the density or the molecular orbitals. As I said, when looking on an iso-surface, my calculated orbitals also look too compact while their shape seems to be OK (as far as this can be seen by visual inspection). After quite carefully checking of my little program I had hoped that there is something about the norm of the orbitals in molden files that I did not consider yet. If this is not the case, I will have to continue debugging in more detail. Thanks anyway Markus