From owner-chemistry@ccl.net Mon Apr 3 10:17:01 2006 From: "alberto savoini alberto.savoini%polimerieuropa.com" To: CCL Subject: CCL:G: g03 and tcp-linda Message-Id: <-31389-060403095630-4577-lky+hEg5/08k3IUVy/1BDw(a)server.ccl.net> X-Original-From: "alberto savoini" Date: Mon, 3 Apr 2006 09:56:28 -0400 Sent to CCL by: "alberto savoini" [alberto.savoini ~~ polimerieuropa.com] Dear all, I' m trying to bild g03 ( Gaussian rev c.01 ) with linda ( 7.1 ) for my cluster with fedora core 3 and PGI 6.1 but I receive this error message: flc (V7.1 LindaTcp) /opt2/g03_fedora/g03/linda7.1/intel-linux2.4/lib/ltcp_linda.a(largs.o)(.text+0x499): In function `ext_get_arg': /sca/homes/daya/linda/ikernel-tcp/largs.c:235: undefined reference to `__ctype_b The single node version of g03 installed successfully. Last year when I was using Red Hat 9 and PGI 4.1 I had no problem. Can you help me ? Thank you for your help. Alberto Savoini Polimeri Europa S.p.A - Istituto Guido Donegani Via Fauser,4 - 28100 Novara (NO) - Italy Tel. : +39 0321 447505 - Fax : +39 0321 447679 email : alberto.savoini]*[PolimeriEuropa.com From owner-chemistry@ccl.net Mon Apr 3 10:51:01 2006 From: "Alessandro - Curioni cur^^^zurich.ibm.com" To: CCL Subject: CCL: New CPMD version 3.11.1 available for download at www.cpmd.org Message-Id: <-31390-060403101848-7687-0nYNsKKITqbIeMhN4jwGhQ[-]server.ccl.net> X-Original-From: "Alessandro - Curioni" Date: Mon, 3 Apr 2006 10:18:45 -0400 Sent to CCL by: "Alessandro - Curioni" [cur,zurich.ibm.com] Dear collegues, with the following I would like to announce the distribution from www.cpmd.org of the new CPMD version 3.11.1. Many improvements, cleanups, bug fixes and some new features have been added since the last public version of the code. New functionalities include: Calculation of electric field gradient tensor along MD trajectory EPR calculations Efficient wavefunction extrapolation for BOMD Distance screening for HFX calculation and hybrid funcional for PBC Interaction perturbation method Molecular states in TDDFT calculations Analytic second derivatives of GC XC functionals Born Charge tensor during FD vibrational analysis Gromacs QM/MM interface Distributed linear algebra New code porting include: IBM Blue Gene/L Cray XT3 Windows NT/XT using gnu gfortran Performance tunings include: FFTW interface Extension of Taskgroup implementation, Cartesian Taskgroups Parallel distributed linear algebra Alltoall communication in single/double precision Special parallel OPEIGR Improved OpenMP support Improved metadynamics On top of this, we have extended/debugged the cpmd2cube utility, extended the CPMD-tests - including examples of different strategies for parallel runs updated and cleaned the manual Thank you very much to all the people contributed to this release - Happy computing Alessandro Curioni for the CPMD Team From owner-chemistry@ccl.net Mon Apr 3 11:26:01 2006 From: "David Santos Carballal david^-^fq.uh.cu" To: CCL Subject: CCL: XYZ to PDB translation Message-Id: <-31391-060331162031-4481-0PXXPQNPcNqCtIq+T6tAPw a server.ccl.net> X-Original-From: David Santos Carballal Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 31 Mar 2006 06:07:47 -0500 (CST) MIME-Version: 1.0 Sent to CCL by: David Santos Carballal [david/./fq.uh.cu] Yes, I know another utility. Try with xyzpdb tool of TINKER, you can download it as an executable or into the full molecular modelling package for windows or linux from its web site, there is avaible the source code in fortran. The web site is http:/dasher.wustl.edu/tinker/ David Santos Carballal On Fri, 31 Mar 2006, Mikhail Ladanov mladanov:mail.usf.edu wrote: > Sent to CCL by: "Mikhail Ladanov" [mladanov/./mail.usf.edu] > I work with MD simulations of system with very big number of atoms. > Im trying to translate my XYZ file into PDB using OpenBabel 2.0 > As soon as I have a file of size about 15-20 Mb, Babel results with segmentation fault. > I have therefore 2 questions: > 1. Is there any way to make OpenBabel work with big files without any errors? > 2. Is there any other utility I could translate XYZ to PDB with?> > > From owner-chemistry@ccl.net Mon Apr 3 12:03:00 2006 From: "Schrodinger Announcements announce ~~ schrodinger.com" To: CCL Subject: CCL: Schrodinger Spring Webinars Message-Id: <-31392-060403120114-8070-BkHH/lMjD7Z4aERGWsahEg++server.ccl.net> X-Original-From: Schrodinger Announcements Date: Mon, 03 Apr 2006 11:13:35 -0400 Sent to CCL by: Schrodinger Announcements [announce() schrodinger.com] Schrodinger is pleased to announce a new series of webcast seminars for spring 2006. With featured speakers that include Schrodinger product managers and applications scientists, the seminars will cover a wide variety of topics including software development, methodology, applications, and usage. The schedule for the first half of the seminar series is given below. To learn more, and to see the full abstracts, please visit our website at: http://www.schrodinger.com/SeminarCenter.php?mID=8&sID=53&cID=0 Date/Time Seminar --------- ----------------------------------------------------------- 4/6/2006 Combining quantum chemistry and classical physics 1 PM EDT modeling: Using mixed QM/MM methods to obtain an atomically detailed view of biological processes Presented by Professor Victor Guallar Washington University at St. Louis 4/13/2006 An introduction to Jaguar: Using the Maestro 1 PM EDT interface to set up and interpret the results of ab intio calculations Presented by Jason K. Perry Schrodinger Applications Scientist 4/20/2006 Schrodinger Induced Fit Docking: 1 PM EST Methodology and results Presented by Woody Sherman, Ph.D. Schrodinger Director of Applications Science 4/27/2006 Python scripting within Maestro 10 AM EST An introductory workshop Presented by Woody Sherman, Ph.D. Schrodinger Director of Applications Science The seminars will run for approximately one hour, including time for questions and answers. The number of connections is limited, so please register early at http://www.schrodinger.com/Spring2006Webinars.html to ensure your participation. Sincerely, Mike Campbell Schrodinger Seminar Coordinator From owner-chemistry@ccl.net Mon Apr 3 12:54:01 2006 From: "Pierre Archirel pierre.archirel|lcp.u-psud.fr" To: CCL Subject: CCL:G: quadrupoles in G03 Message-Id: <-31393-060403123653-29041-9ZBvrVZTzxE/BeRoZ6Ga8Q(!)server.ccl.net> X-Original-From: Pierre Archirel Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 03 Apr 2006 17:44:38 +0200 MIME-Version: 1.0 Sent to CCL by: Pierre Archirel [pierre.archirel|-|lcp.u-psud.fr] Dear Robert, I have recently noticed that what gaussian calls "traceless quadupole moment" is given by: Qzz=-(1/3) which is (2/3) times the quadrupole, as defined by Buckingham: Q(Buck.)=-(1/2)-(1/2) Pierre __________________________________________________________ Pierre Archirel Groupe de Chimie Théorique Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay Cedex France pierre.archirel%lcp.u-psud.fr __________________________________________________________ From owner-chemistry@ccl.net Mon Apr 3 13:54:01 2006 From: "Serena Povia sp422(~)hermes.cam.ac.uk" To: CCL Subject: CCL:G: g03 and tcp-linda Message-Id: <-31394-060403113553-24213-Nw3lMYBxZGm/XS/b86tN0g[A]server.ccl.net> X-Original-From: Serena Povia Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 3 Apr 2006 15:31:00 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: Serena Povia [sp422() hermes.cam.ac.uk] dear Alberto, I've never used G03 but in general such a problem could be solved using the command $ ldd executable that will give you the list of libraries on which the executable depends. At that point you just need to be sure that you have them all. If still it doesn't work I've no better advices. cheers, serena On Mon, 3 Apr 2006, alberto savoini alberto.savoini%polimerieuropa.com wrote: > Sent to CCL by: "alberto savoini" [alberto.savoini ~~ polimerieuropa.com] > Dear all, > > I' m trying to bild g03 ( Gaussian rev c.01 ) with linda ( 7.1 ) for my cluster with fedora core 3 and PGI 6.1 but I receive this error message: > > flc (V7.1 LindaTcp) > /opt2/g03_fedora/g03/linda7.1/intel-linux2.4/lib/ltcp_linda.a(largs.o)(.text+0x499): In function `ext_get_arg': > /sca/homes/daya/linda/ikernel-tcp/largs.c:235: undefined reference to `__ctype_b > > The single node version of g03 installed successfully. > > Last year when I was using Red Hat 9 and PGI 4.1 I had no problem. > > Can you help me ? > > Thank you for your help. > > Alberto Savoini > > Polimeri Europa S.p.A - Istituto Guido Donegani > Via Fauser,4 - 28100 Novara (NO) - Italy > Tel. : +39 0321 447505 - Fax : +39 0321 447679 > email : alberto.savoini() PolimeriEuropa.com> > > > From owner-chemistry@ccl.net Mon Apr 3 14:29:01 2006 From: "Xiaojian Mao mxiaojia===mix.wvu.edu" To: CCL Subject: CCL: Compiling GAMESS - Help Needed Message-Id: <-31395-060403121744-14277-ND5QMa9A0JucFBORaK/eFA_+_server.ccl.net> X-Original-From: "Xiaojian Mao" Date: Mon, 3 Apr 2006 12:17:43 -0400 Sent to CCL by: "Xiaojian Mao" [mxiaojia+*+mix.wvu.edu] Dear CCLers, I am setting up GAMESS on a 64-bit machine. However, I ended up with a problem and cannot solve it. I would be very, very thankful if you can give me some suggestion. I will try to state the problem as clear as possible. 1) Basic Information: The operating system is Linux (Fedora Core 5). The CPU is AMD 64-bit (dual core). I set AMD64 as the TARGET, and the compiler is the PGI 6.1 (pgf77/pgcc) from the Portland Group. 2) DDI Compiling: DDI was compiled by pgcc successfully. The library file libddi.a and the kick program ddikick.x were generated. There are two warnings though. They are: Compiling DDI object: ddi_sync.o pgcc -DLINUX -fastsse -Mipa=fast,safe -I./include -DDDI_SOC -DUSE_SYSV -DMAX_SMP_PROCS=1 -DMAX_NODES=1 -c ./src/ddi_sync.c -o ./obj/ddi_sync.o PGC-W-0136-Function DDI_Sync has non-prototype declaration in scope (./src/ddi_sync.c: 19) PGC/x86-64 Linux/x86-64 6.1-2: compilation completed with warnings unset echo Finished compiling: ddi_sync.o Compiling ddikick object: finalize_tasks.o pgcc -DLINUX -fastsse -Mipa=fast,safe -I./include -DDDI_SOC -DUSE_SYSV -DMAX_SMP_PROCS=1 -DMAX_NODES=1 -c ./tools/ddikick/finalize_tasks.c -o ./obj/finalize_tasks.o PGC-W-0136-Function Finalize_tasks has non-prototype declaration in scope (./tools/ddikick/finalize_tasks.c: 18) PGC/x86-64 Linux/x86-64 6.1-2: compilation completed with warnings unset echo Finished compiling: finalize_tasks.o 3) GAMESS Source Code Compiling: The source code was compiled by pgf77 successfully. No error or warnings were found in the log file. 4) Linking: I had a problem here. I cannot get the executable image gamess.01.x by running lked script. The log file told me that a lot of symbols were undefined. I found all these symbols in the library libgcc_eh.a. So I added -lgcc_eh to the link and got the executable image games.01.x. There was a warning though: ./ddi/libddi.a(std_system.o)(.text+0x75): In function `Gethostbyname': std_system.c: warning: Using 'gethostbyname' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking 5) Running: So here is the problem: I tried to run the example files. The program runs, but always quit right before two electron integrals. The same input example file was test under windows and there is no problem at all. The partial output is like this: ---------------------- AO INTEGRAL TECHNOLOGY ---------------------- S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR). S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE). S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5, ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER). S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY). -------------------- 2 ELECTRON INTEGRALS -------------------- But what I got under the Linux machine is: ---------------------- AO INTEGRAL TECHNOLOGY ---------------------- S,P,L SHELL ROTATED AXIS INTEGRALS, REPROGRAMMED BY KAZUYA ISHIMURA (IMS) AND JOSE SIERRA (SYNSTAR). S,P,D,L SHELL ROTATED AXIS INTEGRALS PROGRAMMED BY KAZUYA ISHIMURA (INSTITUTE FOR MOLECULAR SCIENCE). S,P,D,F,G SHELL TO TOTAL QUARTET ANGULAR MOMENTUM SUM 5, ERIC PROGRAM BY GRAHAM FLETCHER (ELORET AND NASA ADVANCED SUPERCOMPUTING DIVISION, AMES RESEARCH CENTER). S,P,D,F,G,L SHELL GENERAL RYS QUADRATURE PROGRAMMED BY MICHEL DUPUIS (PACIFIC NORTHWEST NATIONAL LABORATORY). ddikick.x: application process 0 quit unexpectedly. ddikick.x: Fatal error detected. The error is most likely to be in the application, so check for input errors, disk space, memory needs, application bugs, etc. ddikick.x will now clean up all processes, and exit... DDI Process 1: terminated upon request. ddikick.x: Sending kill signal to DDI processes. ddikick.x: Execution terminated due to error(s). unset echo 6) Other Useful Information: The execution is set to be sequential (ncpus=1). The SYSV memory limits were took cared (raised to 1G). I changed the exetpy of the example to check to avoid the actual two electron integrals. However, the program quit at exactly the same point (giving the same error). I totally have no idea where I messed things up. I would be great thankful if you can give me some suggestion. Thanks a lot, Mao mxiaojia-x-mix.wvu.edu From owner-chemistry@ccl.net Mon Apr 3 15:04:00 2006 From: "Kirk Beebe kbeebe/a\scripps.edu" To: CCL Subject: CCL: Autodock msmsCommands error Message-Id: <-31396-060331145356-27579-2JX7+F8Y15TXmMuPf+bhSg(0)server.ccl.net> X-Original-From: "Kirk Beebe" Date: Fri, 31 Mar 2006 14:53:56 -0500 Sent to CCL by: "Kirk Beebe" [kbeebe[A]scripps.edu] I am installing autodock on mac OSX (10.4) and everything seems to have gone smoothly after working through several previous rough spots but now I seem to have a problem with the MSMS command file: >>> ERROR ********************************************* Traceback (most recent call last): File "/Applications/MGLTools/share/lib/python2.4/site-packages/ViewerFramework/VF.py", line 652, in tryto result = apply( command, args, kw ) File "/Applications/MGLTools/share/lib/python2.4/site-packages/Pmv/msmsCommands.py", line 509, in checkDependencies import mslib ImportError: No module named mslib WARNING: dependency check failed for command computeMSMS skipping the isocontour-dependent commands I am a beginner whith unix based environments and to Autodock so can anyone give me suggestions for fixing this problem. Than you in advance Kirk From owner-chemistry@ccl.net Mon Apr 3 15:39:00 2006 From: "Tammy Welshman compchem-$-hotmail.com" To: CCL Subject: CCL: Exploding .rwf files in G03 Message-Id: <-31397-060403125915-2058-hr8+J145X8UKa9j46gT3lg _ server.ccl.net> X-Original-From: "Tammy Welshman" Date: Mon, 3 Apr 2006 12:59:14 -0400 Sent to CCL by: "Tammy Welshman" [compchem()hotmail.com] Hi all, I have recently started geometry opt and freq calculations on large (60+ atom) systems. My problem is the huge size of the .rwf file...I had one recently that reached 42GB before running out of disk space. I am using B3LYP/6-31+G**. Anyone have any idea why the .rwf are getting SO huge?? T. From owner-chemistry@ccl.net Mon Apr 3 16:14:00 2006 From: "Jan Labanowski janl%%speakeasy.net" To: CCL Subject: CCL: CINF Scholarship for Scientific Excellence Message-Id: <-31398-060403135825-1626-F5J5nz2XhaVy5a71LFwYFQ_+_server.ccl.net> X-Original-From: "Jan Labanowski" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 03 Apr 2006 17:58:21 +0000 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [janl..speakeasy.net] ---------------------------- Original Message ---------------------------- Subject: CINF Scholarship for Scientific Excellence > From: "Osman Guner" Date: Mon, April 3, 2006 1:44 am To: chemistry-request() ccl.net -------------------------------------------------------------------------- Posted on behalf of Guenter Grethe The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by FIZ CHemie Berlin is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. Three scholarships valued at $1,000 each will be given out at the 232nd ACS National Meeting In San Francisco, September 10 ? 14, 2006. Applicants have to be enrolled at a certified college or university. They have to present a poster during the Sci-Mix session at the National Meeting. Abstracts for the poster have to be submitted electronically through OASYS (http://oasys.acs.org/oasys.htm) according to ACS rules before May 5, 2006. Additionally, a 2,000-word long abstract describing the work to be presented has to be sent in electronic form to the Chair of the selection committee Guenter Grethe at ggrethe() comcast.net byJune 15, 2006. Any questions related to applying for one of the scholarships should be directed to the same e-mail address. Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced at the meeting. The contents shall reflect upon the student?s work and describe research in the field of cheminformatics and related sciences. Winning posters will be marked ?Winner of the CINF-FIZ Chemie Berlin Academic Scientific Excellence? at the poster session. Guenter Grethe Osman F, Güner, PhD Principal, Turquoise Consulting oguner() turquoisecons.com http://www.turquoisecons.com From owner-chemistry@ccl.net Mon Apr 3 16:49:00 2006 From: "Maciej Haranczyk maharan:_:chem.univ.gda.pl" To: CCL Subject: CCL: program to calculate Frank-Condon factors Message-Id: <-31399-060403154418-9825-AnVNV+5trXLYwL7m4mI6kA],[server.ccl.net> X-Original-From: Maciej Haranczyk Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Mon, 3 Apr 2006 20:44:40 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Maciej Haranczyk [maharan._-_.chem.univ.gda.pl] Dear All, I would like to simulate photoelectron spectrum of small anionic molecule. I am looking for a program to calculate Frank-Condon factors in the multidimentional case. Could anyone recommend me such program ? I know there was a program by professor P-N Roy but I am not able to contact professor Roy nor can I find the program on the web. Any help will be appreciated. Thanks, Maciej -- Maciek Haranczyk maharan_-_chem.univ.gda.pl From owner-chemistry@ccl.net Mon Apr 3 17:24:01 2006 From: "Gon alo Justino goncalo.justino]*[zmail.pt" To: CCL Subject: CCL:G: Gaussian and Se Message-Id: <-31400-060403162959-10216-jW4mtityKirPmvh88S6b9A**server.ccl.net> X-Original-From: "Gon alo Justino" Date: Mon, 3 Apr 2006 16:29:58 -0400 Sent to CCL by: "Gon alo Justino" [goncalo.justino]=[zmail.pt] Dear all, I'm ussing Gaussian03 (Win) for some calculations (generally basis/method Opt Freq P)on aromatic compounds with an oxo function, and replacing the =O for a =S and for a =Se. Everything goes smoothly for the first two, but with Se any calculation ends at any time with the message " Error termination request processed by link 9999. Error termination via Lnk1e in l9999.exe at Mon Apr ". I can't find any explanation for this; it occurs with any method/basis combination, including SE methods. Any help would be welcome! Cheers, Gonalo Justino goncalo.justino[]zmail.pt From owner-chemistry@ccl.net Mon Apr 3 17:59:00 2006 From: "Dr. N. SUKUMAR nagams++rpi.edu" To: CCL Subject: CCL:G: Summing Electron Density Message-Id: <-31401-060403161229-28501-J8kLAWlb7xpGIGKf7hY5yA===server.ccl.net> X-Original-From: "Dr. N. SUKUMAR" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Mon, 03 Apr 2006 14:55:05 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. N. SUKUMAR" [nagams#rpi.edu] ==============Original message text=============== On Sat, 01 Apr 2006 22:17:37 EST "Rajan Vatassery r-vatassery a northwestern.edu" wrote: Sent to CCL by: "Rajan Vatassery" [r-vatassery()northwestern.edu] r-vatassery a northwestern.edu Dear CCLers, I am working on a problem involving high harmonic generation and I have the need for a very accurate assessment of the spatial electron distribution in the HOMO of N2 and the HOMO of O2. I have calculated the structures of both (trivially) using GAMESS-US and I plan on summing up the contributions of each basis function (from 6-31++G**) to each HOMO. I have read Dr Labanowski's document at http://www.ccl.net/cca/documents/basis-sets/basis.html but I still have a few small concerns that I may be doing something wrong. First, according to the GAMESS .log file, in the 6-31++G** basis set for O2, I have 19 basis functions per oxygen, where I only count 17 in the basis set coefficient numbers listed here (parentheses and numbers inside are my count): SHELL TYPE PRIMITIVE EXPONENT CONTRACTION COEFFICIENT(S) O 6 S 1 5484.6716600 0.001831074430(1) 6 S 2 825.2349460 0.013950172200(2) 6 S 3 188.0469580 0.068445078098(3) 6 S 4 52.9645000 0.232714335992(4) 6 S 5 16.8975704 0.470192897984(5) 6 S 6 5.7996353 0.358520852987(6) 7 L 7 15.5396162 -0.110777549525(7) 0.07087426(13) 7 L 8 3.5999336 -0.148026262701(8) 0.33975283(14) 7 L 9 1.0137618 1.130767015354(9) 0.72715857(15) 8 L 10 0.2700058 1.000000000000(10)1.00000000(16) 9 L** 11 0.0845000 1.000000000000(11)1.00000000(17) 10 D 12 0.8000000 1.000000000000(12) This is obviously a simple error on my part, but I'm sure someone else has made the same mistake. If you have, could you please let me know what is wrong, or point me to resources that have helped you? Secondly, and finally, I don't know what the last L function (the one with the double asterisk) is referring to. I can assume it's a diffuse function, but I can't find the coefficient in my .log file that would match it in my O2 molecule. I can see from Dr Labanowski's document that the 'S' in my .log file corresponds to the spherically symmetric function (any of 1-6 numbered above), and that the 'Y' corresponds to the spherically symmetric function (any of 13-16) times displacement along y, but I can't figure out which coefficient in my .log file goes with the last 'L' (11 or 17). Any help is greatly appreciated. Rajan Vatassery Graduate Student ===========End of original message text=========== 19 functions for O is correct in the 6-31++G** basis: #1) Core 1S orbital contracted from 6 primitive Gaussians (S primitives 1-6). #2-5) Valence S, px, py & pz orbitals, contracted from 3 primitive Gaussians (L primitives 7-9). #6-9) Another set of Valence S, px, py & pz orbitals, each from the single L primitives 10. #10-13) A set of diffuse S, px, py & pz orbitals, each from the single L primitive 11. #14-19) A set of six D polarization functions constructed from D primitive 12. For details see the output below from Gaussian98. The second * in 6-31++G** does not apply in your case; it refers to a polarization functions on hydrogen. Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute Standard basis: 6-31++G(d,p) (6D, 7F) *********************************************************************************************************************************** * ATOMIC CENTER * ATOMIC ORBITAL * GAUSSIAN FUNCTIONS * *********************************************************************************************************************************** * * FUNCTION SHELL SCALE * * * ATOM X-COORD Y-COORD Z-COORD * NUMBER TYPE FACTOR * EXPONENT S-COEF P-COEF D-COEF F-COEF * *********************************************************************************************************************************** * O 0.00000 0.00000 1.41729 * + 1 S 1.00 + 0.548467D+040.183107D-020.000000D+000.000000D+000.000000D+00 * 0.825235D+030.139502D-010.000000D+000.000000D+000.000000D+00* * 0.188047D+030.684451D-010.000000D+000.000000D+000.000000D+00* * 0.529645D+020.232714D+000.000000D+000.000000D+000.000000D+00* * 0.168976D+020.470193D+000.000000D+000.000000D+000.000000D+00* * 0.579964D+010.358521D+000.000000D+000.000000D+000.000000D+00* * 2- 5 SP 1.00 * + 0.155396D+02-.110778D+000.708743D-010.000000D+000.000000D+00 * 0.359993D+01-.148026D+000.339753D+000.000000D+000.000000D+00* * 0.101376D+010.113077D+010.727159D+000.000000D+000.000000D+00* * 6- 9 SP 1.00 * + 0.270006D+000.100000D+010.100000D+010.000000D+000.000000D+00 * 10- 13 SP 1.00 * + 0.845000D-010.100000D+010.100000D+010.000000D+000.000000D+00 * 14- 19 6D 1.00 * + 0.800000D+000.000000D+000.000000D+000.100000D+010.000000D+00 *---------------------------------------------------------------------------------------------------------------------------------* From owner-chemistry@ccl.net Mon Apr 3 18:34:01 2006 From: "Nuno A. G. Bandeira nuno.bandeira : ist.utl.pt" To: CCL Subject: CCL:G: Gaussian and Se Message-Id: <-31402-060403175645-26292-GDTdd0/dUA6SHAn0iupE/Q||server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Date: Mon, 3 Apr 2006 17:56:40 -0400 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira-.-ist.utl.pt] Gon alo Justino goncalo.justino]*[zmail.pt wrote: > Sent to CCL by: "Gon alo Justino" [goncalo.justino]=[zmail.pt] > Dear all, > > I'm ussing Gaussian03 (Win) for some calculations (generally basis/method Opt Freq P)on aromatic compounds with an oxo function, and replacing the =O for a =S and for a =Se. Everything goes smoothly for the first two, but with Se any calculation ends at any time with the message " Error termination request processed by link 9999. Error termination via Lnk1e in l9999.exe at Mon Apr ". I can't find any explanation for this; it occurs with any method/basis combination, including SE methods. Any help would be welcome! Please show us your input/output file. Did you turn off the text output (blue) window ? Explorer finds problems with it sometimes. -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student ~~ IST,Lisbon -- From owner-chemistry@ccl.net Mon Apr 3 19:09:00 2006 From: "Joslyn Y Kravitz jyudenfr=-=umich.edu" To: CCL Subject: CCL: XYZ to PDB translation Message-Id: <-31403-060331154630-861-TiJbdoUoZ+PmcExQvaT33g:+:server.ccl.net> X-Original-From: Joslyn Y Kravitz Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 31 Mar 2006 15:05:13 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Joslyn Y Kravitz [jyudenfr]=[umich.edu] This is a perfect application of perl- a short script will read in the xyz coordinates and then print them out with whatever spacing you specify. PDB format can be found at http://pdbdev.sdsc.edu:48346/pdb/docs/format/pdbguide2.2/guide2.2_frame.html On Fri, 31 Mar 2006, Mikhail Ladanov mladanov:mail.usf.edu wrote: > Sent to CCL by: "Mikhail Ladanov" [mladanov/./mail.usf.edu] > I work with MD simulations of system with very big number of atoms. > Im trying to translate my XYZ file into PDB using OpenBabel 2.0 > As soon as I have a file of size about 15-20 Mb, Babel results with segmentation fault. > I have therefore 2 questions: > 1. Is there any way to make OpenBabel work with big files without any errors? > 2. Is there any other utility I could translate XYZ to PDB with?> > > > > > From owner-chemistry@ccl.net Mon Apr 3 20:09:00 2006 From: "Matt Thompson thompsma/./jilau1.Colorado.EDU" To: CCL Subject: CCL: program to calculate Frank-Condon factors Message-Id: <-31404-060403183941-25520-KUvnffpA4+78ZdwjpQR9TQ**server.ccl.net> X-Original-From: Matt Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 03 Apr 2006 15:34:40 -0600 MIME-Version: 1.0 Sent to CCL by: Matt Thompson [thompsma(0)jilau1.Colorado.EDU] Maciej Haranczyk maharan:_:chem.univ.gda.pl wrote: > Sent to CCL by: Maciej Haranczyk [maharan.:_:.chem.univ.gda.pl] > Dear All, > > I would like to simulate photoelectron spectrum of small anionic molecule. > I am looking for a program to calculate Frank-Condon factors in the > multidimentional case. Could anyone recommend me such program ? > > I know there was a program by professor P-N Roy but I am not able to > contact professor Roy nor can I find the program on the web. > > Any help will be appreciated. Here is a link to Prof. Le Roy's LEVEL program: http://scienide.uwaterloo.ca/~leroy/level/ Note, though, I think LEVEL is for one-dimensional or radial potentials. This may not be what you want. Matt -- root *is* my user account! Matt Thompson -- http://ucsub.colorado.edu/~thompsma/ 440 UCB, Boulder, CO 80309-0440 JILA A510, 303-492-4662 From owner-chemistry@ccl.net Mon Apr 3 22:14:00 2006 From: "=?ISO-8859-1?Q?Carlos_Javier_Nu=F1ez_Aguero?= carlosjn|-|ce.fis.unam.mx" To: CCL Subject: CCL: Forcefield parameters for beta-cyclodextrin Message-Id: <-31405-060403143350-21335-pKOSwMJQ8w/jzq/xZm2oZA[a]server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Carlos_Javier_Nu=F1ez_Aguero?= Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 03 Apr 2006 12:57:58 -0500 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Carlos_Javier_Nu=F1ez_Aguero?= [carlosjn_+_ce.fis.unam.mx] Hi all, In AMBER you can use the parameters of the GLYCAM-x (x = 93, 95) force field. In AMBER-y (y = 7, 8, 9) you have two options to generate the *.top and *.crd files: i.- using LEaP ii.- maybe you can find help in "AMBER/GLYCAM Input Configurator" http://glycam.ccrc.uga.edu/ or http://amber.scripps.edu/ You have to make tests in this point. I hope this helps Hasta la proxima ocasion, Carlos N. -------------------------------- http://www.uaem.mx/ http://www.ciq.uaem.mx/ http://www.ibt.unam.mx http://www.puertodetampico.com.mx/ http://www.tampico-online.com/ Sanjoy Bandyopadhyay sanjoy]^[chem.iitkgp.ernet.in wrote: >Sent to CCL by: Sanjoy Bandyopadhyay [sanjoy- -chem.iitkgp.ernet.in] >Dear All, > >I am looking for the topology and forcefield parameters for >beta-cyclodextrin. Any help will be appreciated. > >Thanks. >Sanjoy > > > > -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.385 / Virus Database: 268.3.4/299 - Release Date: 3/31/2006 From owner-chemistry@ccl.net Mon Apr 3 22:48:01 2006 From: "Sue L chsue2004/./yahoo.com" To: CCL Subject: CCL: TDDFT for Large Unsaturated pi-Systems Message-Id: <-31406-060403224551-31582-OR8sA4BaQwT9nErVHbPVbA~~server.ccl.net> X-Original-From: "Sue L" Date: Mon, 3 Apr 2006 22:45:48 -0400 Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] Does anyone know which DFT functional in TDDFT is suitable to calculate the singlet-singlet excitations for large unsaturated pi-systems? B3LYP usually underestimate the excitation energies for these systems Thank you very much Sue