From owner-chemistry@ccl.net Mon Jun 30 10:21:00 2008 From: "Robert Kolakowski rkolakow{=}rci.rutgers.edu" To: CCL Subject: CCL:G: Hessian Matrix Output for G03 Message-Id: <-37275-080630071420-6172-CWjJuFNrIM0vTRYF8TofBw:-:server.ccl.net> X-Original-From: "Robert Kolakowski" Date: Mon, 30 Jun 2008 07:14:16 -0400 Sent to CCL by: "Robert Kolakowski" [rkolakow a rci.rutgers.edu] Dear colleagues, How do you display the Hessian matrix for a G03 DFT optimization? Cheers, Robert Kolakowski Department of Chemistry, Rutgers the State University of NJ From owner-chemistry@ccl.net Mon Jun 30 11:02:00 2008 From: "Sarah R Whittleton SWhittleton_-_dal.ca" To: CCL Subject: CCL:G: SCF is confused? Message-Id: <-37276-080630083922-15316-CXsmfGHwDXDZlOVBfyXXXg|server.ccl.net> X-Original-From: "Sarah R Whittleton" Date: Mon, 30 Jun 2008 08:39:18 -0400 Sent to CCL by: "Sarah R Whittleton" [SWhittleton|dal.ca] Hi CCL, I am trying to run a BSSE single-point calculation (counterpoise) using MP2 on an organotin compound. The tin atom is described using the Stuttgart ECP and an augmented, triple-zeta basis set. After running for 11 hours the calculation dies uncompleted and the output (copied below) says that Density matrix is not changing but DIIS error and the SCF is confused. I have run similar calculations with the same method on different organotin compounds and this is the only one giving me trouble. I want to keep the method (MP2) and basis set consistent between compounds is there anything I can do to make resolve this problem and allow the calculations to complete normally? I have also included the first lines of the input file for this calculation. I thank you all in advance for any suggestions, Sarah Whittleton ******************************** Ph.D. Candidate Department of Chemistry Dalhousie University Halifax, NS B3H 4J3 THE END OF THE OUTPUT FILE: The electronic state of the initial guess is 2-A. of initial guess= 0.7500 Requested convergence on RMS density matrix=1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=1.00D-06. Requested convergence on energy=1.00D-06. No special actions if energy rises. Restarting incremental Fock formation. Density matrix is not changing but DIIS error= 1.23D-06 CofLast=-1.58D-02. The SCF is confused. Error termination via Lnk1e in /usr/local/gaussian/g03/l502.exe at Tue Jun 24 22:30:03 2008. Job cpu time: 0 days 11 hours 8 minutes 18.9 seconds. File lengths (MBytes): RWF= 65118 Int= 0 D2E= 0 Chk= 8 Scr= 1 THE INPUT FILE: %mem=2GB %nprocs=3 %chk=MP2-test.chk # MP2/GenECP Pseudo=Read counterpoise=2 maxdisk=200GB From owner-chemistry@ccl.net Mon Jun 30 11:37:00 2008 From: "Remy Fortrie remy.fortrie[]univ-cezanne.fr" To: CCL Subject: CCL:G: "cannot find libmkl_solver_lp64.a" and gau-machine Message-Id: <-37277-080630103019-9331-tTBiu8+PbhqMtVLQJtnA+g=server.ccl.net> X-Original-From: "Remy Fortrie" Date: Mon, 30 Jun 2008 10:30:15 -0400 Sent to CCL by: "Remy Fortrie" [remy.fortrie---univ-cezanne.fr] Dear CCLers, I am currently trying to compile Gaussian 03 on a Xeon (4 core, 64 bits) machine (Intel Fortan compiler). I have two problems/questions: 1. gau-machine was not found. As this program is requested by g03.login, I created one that return i386. It seems to work properly, but I would like to know if this is the proper value for my machine. 2. At the end of the compilation, I got this: ===== /opt/intel/fce/10.1.015/bin/ifort -L/opt/intel/fce/10.1.015/lib -WB -i8 -w -ftz -switch fe_new_cgoto -IPF_fp_relaxed -i-static -IPF_fp_speculationsafe -openmp -fpp2 -auto -O3 -o g03 ml0.o util.a /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_intel_lp64.a /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_sequential.a /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_solver.a /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_lapack.a /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_em64t.a /opt/intel/mkl/10.0.1.014/lib/em64t/libmkl_core.a ld: cannot find libmkl_solver_lp64.a make: *** [g03] Error 1 ===== I tried to change libmkl_solver.a into libmkl_solver_lp64.a in the compilation line, but then I got the following message: ===== ld: cannot find libmkl_intel_lp64.a ===== Which sounds strange since this file is explicitely mentionned in the compilation line !! Has anybody had similar a problem and found a solution ? Thank you for your help Remy From owner-chemistry@ccl.net Mon Jun 30 12:12:01 2008 From: "aa aa(-)chemaxon.hu" To: CCL Subject: CCL: Program Announcement: ChemAxon US UGM and Training. Boston Aug 7-8th and 6th Message-Id: <-37278-080630113917-19459-41vG1VdzTx8GZV0xB9nAeA(!)server.ccl.net> X-Original-From: aa Content-Type: multipart/alternative; boundary="------------070604030205020403020506" Date: Mon, 30 Jun 2008 11:38:39 -0400 MIME-Version: 1.0 Sent to CCL by: aa [aa::chemaxon.hu] This is a multi-part message in MIME format. --------------070604030205020403020506 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Excuse multiple posting We are announcing the program of ChemAxon's first US User Group Meeting to take place in Boston, MA, August 7-8. Please note also our developer and end user training day on Aug 6th, preceding the meeting. I hope you agree that we will have a rich and varied range of user and ChemAxon topics, see user presentations below. Note also that the Meeting Mixer, with the robots at MIT Museum, on the evening of Wednesday 6th is open to both training and UGM attendees as is the informal get together on Thursday 7th. Hope you can join us for what has been a stimulating and enjoyable event in Europe and a valuable opportunity to meet and discuss with peers and ChemAxon staff. See you in Boston Alex Program: http://www.chemaxon.com/UGM/08/US/program_usa.html Registration and poster submission: http://www.chemaxon.com/ugm.php Information page: http://www.chemaxon.com/UGM/08/index.html Training day topics: http://www.chemaxon.com/training/0808.html *User Presentations:* * Derek A. Debe, *Abbott Laboratories*: /Clustering for the Masses: Pairing JKlustor with Seurat / * Peter Condron, *ETC, A-STAR*: /ChemAxon and an Electronic Research Habitat at the Biopolis Experimental Research Centre/ * Kaisheng Chen, *Genomics Institute of the Novartis Research Foundation*: /Large-Scale Annotation of Small-Molecule Libraries Using Public Databases/ * Trung Nguyen, *NIH Chemical Genomics Center (NCGC)*: /Toward the Development of an Open Source Cheminformatics Platform for HTS Data Analysis and Visualization/ * Lutz Weber, *OntoChem*, /Very large databases and 2D- and 3D-Similarity Searching / * Jim Bullington,* Palatin Technologies*: /Palatin Technologies' Cheminformatics Solution/ * Yao Liu, *Sloan Kettering*: /Successful Implementation of the ChemAxon Chemistry Cartridge in a Custom Built Screening Management Application: A case Study./ * Matthew Pustelnik, *Takeda, San Diego*: /Developing a Compound Registration System utilizing ChemAxon's Oracle Cartridge and incorporating Web 2.0 concepts into research informatics/ * Oleg Ursu, *Div. Biocomputing, U. New Mexico*: /PubChem data extraction and integration using Instant JChem/ * Carlos Fraeman,*Vertex Pharmaceuticals*:/ Instant J Chem: one-stop information hub for medicinal chemists / -- Alex Allardyce Dir. Marketing, ChemAxon --------------070604030205020403020506 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
Excuse multiple posting

We are announcing the program of ChemAxon's first US User Group Meeting to take place in Boston, MA, August 7-8. Please note also our developer and end user training day on Aug 6th, preceding the meeting.

I hope you agree that we will have a rich and varied range of user and ChemAxon topics, see user presentations below.  Note also that the Meeting Mixer, with the robots at MIT Museum, on the evening of Wednesday 6th is open to both training and UGM attendees as is the informal get together on Thursday 7th.

Hope you can join us for what has been a stimulating and enjoyable event in Europe and a valuable opportunity to meet and discuss with peers and ChemAxon staff.

See you in Boston
Alex

Program: http://www.chemaxon.com/UGM/08/US/program_usa.html
Registration and poster submission: http://www.chemaxon.com/ugm.php
Information page: http://www.chemaxon.com/UGM/08/index.html
Training day topics: http://www.chemaxon.com/training/0808.html

User Presentations:
* Derek A. Debe, Abbott Laboratories: Clustering for the Masses: Pairing JKlustor with Seurat
* Peter Condron, ETC, A-STAR: ChemAxon and an Electronic Research Habitat at the Biopolis Experimental Research Centre
* Kaisheng Chen, Genomics Institute of the Novartis Research Foundation: Large-Scale Annotation of Small-Molecule Libraries Using Public Databases
* Trung Nguyen, NIH Chemical Genomics Center (NCGC): Toward the Development of an Open Source Cheminformatics Platform for HTS Data Analysis and Visualization
* Lutz Weber, OntoChem, Very large databases and 2D- and 3D-Similarity Searching
* Jim Bullington, Palatin Technologies: Palatin Technologies’ Cheminformatics Solution
* Yao Liu, Sloan Kettering: Successful Implementation of the ChemAxon Chemistry Cartridge in a Custom Built Screening Management Application: A case Study.
* Matthew Pustelnik, Takeda, San Diego: Developing a Compound Registration System utilizing ChemAxon's Oracle Cartridge and incorporating Web 2.0 concepts into research informatics
* Oleg Ursu, Div. Biocomputing, U. New Mexico: PubChem data extraction and integration using Instant JChem
* Carlos Fraeman,Vertex Pharmaceuticals: Instant J Chem: one-stop information hub for medicinal chemists

 
-- 
Alex Allardyce
Dir. Marketing, ChemAxon

--------------070604030205020403020506-- From owner-chemistry@ccl.net Mon Jun 30 23:51:00 2008 From: "McGaughey, Georgia B. georgia_mcgaughey*|*merck.com" To: CCL Subject: CCL:G: SCF is confused? Message-Id: <-37279-080630122112-18696-7dzwJTqtVCvYrEDS6BOTJA],[server.ccl.net> X-Original-From: "McGaughey, Georgia B." Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Mon, 30 Jun 2008 11:46:47 -0400 MIME-Version: 1.0 Sent to CCL by: "McGaughey, Georgia B." [georgia_mcgaughey{}merck.com] Sarah, Have you tried any other key words? For calculating dimer interactions using MP2/aug-cc-pvdz, I typically use the Counterpoise=3D2 keyword (in Gaussian) along w/ SCF=3D(qc,tight,maxcycle=3D512). I too had "SCF is confused" in my output on occasion prior to adding in the SCF syntax. -Georgia=20 -----Original Message----- > From: owner-chemistry!=!ccl.net [mailto:owner-chemistry!=!ccl.net]=20 Sent: Monday, June 30, 2008 8:39 AM To: McGaughey, Georgia B. Subject: CCL:G: SCF is confused? Sent to CCL by: "Sarah R Whittleton" [SWhittleton|dal.ca] Hi CCL, I am trying to run a BSSE single-point calculation (counterpoise) using MP2 on an organotin compound. The tin atom is described using the Stuttgart ECP and an augmented, triple-zeta basis set. After running for 11 hours the calculation dies uncompleted and the output (copied below) says that Density matrix is not changing but DIIS error and the SCF is confused. I have run similar calculations with the same method on different organotin compounds and this is the only one giving me trouble. I want to keep the method (MP2) and basis set consistent between compounds is there anything I can do to make resolve this problem and allow the calculations to complete normally? I have also included the first lines of the input file for this calculation. I thank you all in advance for any suggestions, Sarah Whittleton =09 ******************************** Ph.D. Candidate Department of Chemistry Dalhousie University Halifax, NS B3H 4J3 THE END OF THE OUTPUT FILE: The electronic state of the initial guess is 2-A. of initial guess=3D 0.7500 Requested convergence on RMS density matrix=3D1.00D-08 within 128 cycles. Requested convergence on MAX density matrix=3D1.00D-06. Requested convergence on energy=3D1.00D-06. No special actions if energy rises. Restarting incremental Fock formation. Density matrix is not changing but DIIS error=3D 1.23D-06 CofLast=3D-1.58D-02. The SCF is confused. Error termination via Lnk1e in /usr/local/gaussian/g03/l502.exe at Tue Jun 24 22:30:03 2008. Job cpu time: 0 days 11 hours 8 minutes 18.9 seconds. File lengths (MBytes): RWF=3D 65118 Int=3D 0 D2E=3D 0 Chk=3D = 8 Scr=3D 1 THE INPUT FILE: %mem=3D2GB %nprocs=3D3 %chk=3DMP2-test.chk # MP2/GenECP Pseudo=3DRead counterpoise=3D2 maxdisk=3D200GB -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txtNotice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu - direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.