From owner-chemistry@ccl.net Thu Jul 14 07:15:12 2005 From: "CCL" To: CCL Subject: CCL: Multiple basis sets in Gaussian 03 Message-Id: <-28886-050714071230-10518-gJKokDZHWSap5rm98+rrIw###server.ccl.net> X-Original-From: simon archive Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 MIME-Version: 1.0 Sent to CCL by: simon archive Morning Everybody I am starting out on a computational project and need help. I wish to set up an input file for a minimisation and freqency calculation for a platinum complex using Gaussian 03, with two different basis sets. Lanl2dz for Pt and 6-311++g(2d,2p) for Cl and O. A copy of my input file is shown here: %chk=testPtCl2O.chk %mem=256MB %nproc=1 # opt freq rb3lyp gen pseudo=read geom=connectivity PtCl2O opt+freq Pt=lanl2dz C,O=6-311++g(2d,2p) 0 1 Pt Cl 1 B1 Cl 1 B2 2 A1 O 1 B3 3 A2 2 D1 B1 2.28000000 B2 2.28000000 B3 1.95000000 A1 120.00000011 A2 119.99999978 D1 -180.00000000 1 2 1.0 3 1.0 4 1.0 2 3 4 Pt 0 lanl2dz **** Cl O 0 6-311++g(2d,2p) **** I get the following error message in the log file. EOF while reading ECP pointer card. Error termination via Lnk1e in /usr/local/g03/l301.exe Please help me identify the error in my input file. Or if possible, suggest an alternative method for setting up the input file. Any help would be much appreciated. Thanks, Simon ___________________________________________________________ Yahoo! Messenger - NEW crystal clear PC to PC calling worldwide with voicemail http://uk.messenger.yahoo.com From owner-chemistry@ccl.net Thu Jul 14 08:42:08 2005 From: "CCL" To: CCL Subject: CCL: W:Meeting in Philadelphia on Drug Discovery Applications of Cheminf Message-Id: <-28887-050714083527-28823-gJKokDZHWSap5rm98+rrIw]^[server.ccl.net> X-Original-From: "Barry Hardy" Sent to CCL by: "Barry Hardy" eCheminfo US Autumn 2005 InterAction Meeting The eCheminfo US Autumn 2005 meeting will be taking place at Bryn Mawr College, Philadelphia, US, 11-12 October. Program information and registration is available through the eCheminfo website at http://echeminfo.com/ The theme of the meeting is the application of cheminformatics and chemical modelling to drug discovery and will include the following sessions: Virtual Screening, Docking & Scoring, chaired by Max Cummings (Johnson & Johnson); Web-based Services in Drug Design, chaired by Marc Nicklaus, (National Institutes of Health); Protein Folding, Misfolding & Aggregation: Applications to Disease, chaired by Nikolay V. Dokholyan (University of North Carolina); New Developments in Biophysical Applications of Quantum Mechanics, chaired by Ken Merz/Lance Westerhoff (QuantumBio); Simulation of Membranes & Ion Channels, co-chaired by Richard Pastor (FDA) & Michael Klein (University of Pennsylvania) Invited Speakers include: Emanuele Perola (Vertex), Mark McGann (Openeye), John Irwin (UCSF), Renee DesJarlais (Johnson & Johnson), Willem Nissink (Cambridge Crystallographic Data Centre), Brad Feuston (Merck), Brett Tounge (Johnson & Johnson), Steve Bryant (NCBI), David Covell (NCI), Andrew Miranker (Yale University), David Teplow (David Geffen School of Medicine at UCLA), Ron Wetzel (University of Tenessee Medical Center), Michael Thorpe (Arizona State University), Feng Ding (University of North Carolina), Mike Pitman (IBM), Jeff Klauda (NIH), Emad Tajkhorshid (Beckman Institute, University of Illinois at Urbana-Champaign), Richard Pastor (FDA), Preston Moore (USIP), Martin Peters (Penn State), Darrin York (University of Minnesota) The eCheminfo meetings will have exhibitor tables for software demos and evening poster sessions; posters will also be available for viewing through the website. Posters can be on any informatics or modeling topic of relevance to drug discovery. Those who cannot make the meetings are also able to register to access all presentations with audio and posters through the eCheminfo website. Poster Abstracts (ca. 300 words) should be sent to eCheminfo at douglasconnect.com Papers submitted with either seminar or poster presentations will be refereed for consideration for publication in the Molecular Simulation journal. The InnovationWell US community of practice Autumn meeting will be taking place at the same location and on the same dates as the eCheminfo US meeting. This meeting will be covering semantic web applications in drug discovery, personalised medicine, knowledge management and transfer in R&D, clinical trial productivity, drug safety knowledge management and predictive toxicology. All eCheminfo registrants will also have access to the InnovationWell meeting activities. (See http://innovationwell.net/ for more details). What is the eCheminfo Community of Practice? http://echeminfo.com/ eCheminfo is a global Community of Practice (CoP) dedicated to the sharing of research and development of best practices in cheminformatics and chemical modelling of relevance to drug discovery. The CoP involves a diversity of subject matter expertise including experienced professionals from the life science and pharmaceutical industry, vendors, research institutes, universities and government. eCheminfo is committed to the core value of outreach with diverse groups in the commercial, government and academic sectors for the sharing of best practices and the development of strategies, resources and methodologies that address specific issues in improved drug discovery and productivity. Communications activities deploy virtual approaches and a collaboration environment, in addition to regional discussion- and networking-designed face-to-face InterAction meetings. Membership includes access to over 100 seminars from top industry and academic experts, discussion conference calls, and networking facilities. Barry Hardy, PhD Community of Practice Manager Douglas Connect, Switzerland +41 61 851 0170 (office) www.douglasconnect.com From owner-chemistry@ccl.net Thu Jul 14 08:44:51 2005 From: "CCL" server.ccl.net> To: CCL Subject: CCL: W: European Meeting on Drug Discovery, Cheminformatics & Modelling Message-Id: <-28888-050714083755-29595-gJKokDZHWSap5rm98+rrIw<*>server.ccl.net> X-Original-From: "Barry Hardy" tiscalinet.ch> Sent to CCL by: "Barry Hardy" tiscalinet.ch> eCheminfo European Autumn 2005 InterAction Meeting The eCheminfo European Autumn 2005 meeting will be taking place at the Swissotel Lentre Conference Center, Basel, Switzerland, November 9-10. Program information and registration is available through the eCheminfo website at http://echeminfo.com/ The theme of the meeting is the application of cheminformatics and chemical modelling to drug discovery and will include the following sessions: Virtual Screening, Docking & Scoring, chaired by Miklos Vargyas (ChemAxon); Web-based Services in Drug Design, chaired by Kim Henrick (European Bioinformatics Institute); Computational Biochemistry, chaired by Alessandro Curioni (IBM Zurich); Applications of Machine Learning & Graph Mining in Drug Discovery, chaired by Stefan Kramer (Technische Universitaet Muenchen); Biosensors & Nanofluidics, Nick Quirke (Imperial College London); Protein Folding and Dynamics, chaired by Wilfred van Gunsteren (ETH-Zurich) Invited Speakers include: Graham Richards (University of Oxford), Xavier Barril (Vernalis), Amedeo Caflisch (ETH-Zurich), David Morley (Enspiral Discovery Ltd), Didier Rognan (University of Strasbourg), Dimitris Dimitropoulos (European Bioinformatics Institute), Johann Gasteiger (Universitaet Erlangen-Nuernberg), Simon Coles (University of Southampton), Eugene Krissinel (European Bioinformatics Institute), Torsten Schwede (University of Basel), Paul Tavan (University of Munich), Ursula Roethlisberger (Swiss Federal Institute of Technology, Lausanne), Alessandro Curioni (IBM Zurich), Ian Williams (University of Bath), Gerald Monard (Universite Henri Poincare - Nancy), Ken Merz (QuantumBio), Nick Quirke (Imperial College London), Richard Gilbert (E2v Technologies), Andrew De Mello (Imperial College London), Jens Walther (ETH-Zurich), Christoph Helma (University of Freiburg), Peter Willett (University of Sheffield), Joost N. Kok (Leiden University), Gisbert Schneider (Johann Wolfgang Goethe-University), Michael Berthold (University of Konstanz), Jeremy Smith (University of Heidelberg), Wolfgang Wenzel (University of Karslruhe), Thomas Kiefhaber (University of Basel), Xavier Daura (University of Barcelona), Nikolay V. Dokholyan (University of North Carolina), Michele Vendruscolo (University of Cambridge) The eCheminfo meetings will have exhibitor tables for software demos and evening poster sessions; posters will also be available for viewing through the website. Posters can be on any informatics or modeling topic of relevance to drug discovery. Those who cannot make the meetings are also able to register to access all presentations with audio and posters through the eCheminfo website. Poster Abstracts (ca. 300 words) should be sent to eCheminfo at douglasconnect.com Papers submitted with either seminar or poster presentations will be refereed for consideration for publication in the Molecular Simulation journal. The InnovationWell European community of practice Autumn meeting will be taking place at the same location and on the same dates as the eCheminfo European meeting. This meeting will be covering semantic web applications in drug discovery and development, life science intellectual property management and valuation; knowledge management and transfer in R&D and manufacturing, clinical trial productivity, drug safety knowledge management and predictive toxicology. All eCheminfo registrants will also have access to the InnovationWell meeting activities. (See http://innovationwell.net/ for more details). Please register early for the meetings as the number of places are limited. You can register for the meeting on the website or contact Nicki Douglas (nicki.douglas at douglasconnect.com, +41 61 851 0461) to reserve your place. What is the eCheminfo Community of Practice? http://echeminfo.com/ eCheminfo is a global Community of Practice (CoP) dedicated to the sharing of research and development of best practices in cheminformatics and chemical modelling of relevance to drug discovery. The CoP involves a diversity of subject matter expertise including experienced professionals from the life science and pharmaceutical industry, vendors, research institutes, universities and government. eCheminfo is committed to the core value of outreach with diverse groups in the commercial, government and academic sectors for the sharing of best practices and the development of strategies, resources and methodologies that address specific issues in improved drug discovery and productivity. Communications activities deploy virtual approaches and a collaboration environment, in addition to regional discussion- and networking-designed face-to-face InterAction meetings. Membership includes access to over 100 seminars from top industry and academic experts, discussion conference calls, and networking facilities. Barry Hardy, PhD Douglas Connect, Switzerland +41 61 851 0170 (office) www.douglasconnect.com From owner-chemistry@ccl.net Thu Jul 14 12:08:18 2005 From: "CCL" To: CCL Subject: CCL: Problem combining LAN2DZ with 6-31G(d,p) Message-Id: <-28889-050714114840-10353-gJKokDZHWSap5rm98+rrIw() server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet Dear all, I have a problem combining LAN2DZ basis set for Zn with 6-31G(d,p) for other elements in Gaussian. When I optimize the strucure with LAN2DZ as the basis set for all the elements, everything goes fine. The manual states that this basis set is a double-zeta for C, N, O, H. But when I use gen in gaussian and define a 6-31G(d,p) basis set for C, N, O and H and LAN2DZ for Zn, very strange geometries are generated during the optimisation. I get structures with Zn-N distance lower than 1.0A and these structures are lower in energy than the initial one. It is as if all atoms are attracted towards the central Zn. See the enclosed geometries for more detail. Is it because the LAN2DZ pseudopotential cannot be mixed with other basis sets? Or are there other reasons? Is this a common result? Thanks in advance, Ramon Crehuet Gaussian input: %Mem=150Mb #P B3LYP/gen Test Opt scf=(qc,direct) reactiu1H + formiat amb 1 aigua base gran2 1 1 c c 1 cc2 o 2 oc3 1 occ3 zn 3 zno4 2 znoc4 1 dih4 n 4 nzn5 3 nzno5 2 dih5 o 1 oc6 2 occ6 3 dih6 n 4 nzn7 6 nzno7 1 dih7 n 4 nzn8 6 nzno8 1 dih8 o 6 oo9 1 ooc9 2 dih9 c 9 co10 6 coo10 1 dih10 o 10 oc11 9 oco11 6 dih11 o 9 oo12 10 ooc12 11 dih12 h 2 hc13 1 hcc13 6 dih13 h 1 hc14 6 hco14 4 dih14 h 6 ho15 1 hoc15 2 dih15 h 7 hn16 4 hnzn16 6 dih16 h 7 hn17 4 hnzn17 6 dih17 h 7 hn18 4 hnzn18 6 dih18 h 8 hn19 4 hnzn19 6 dih19 h 8 hn20 4 hnzn20 6 dih20 h 8 hn21 4 hnzn21 6 dih21 h 5 hn22 4 hnzn22 6 dih22 h 5 hn23 4 hnzn23 6 dih23 h 5 hn24 4 hnzn24 6 dih24 h 1 hc25 6 hco25 4 dih25 h 10 hc26 9 hco26 6 dih26 h 12 ho27 9 hoo27 10 dih27 h 12 ho28 9 hoo28 10 dih28 cc2 1.484209 oc3 1.264701 occ3 121.076 zno4 2.251448 znoc4 115.693 dih4 -3.279 nzn5 2.141671 nzno5 158.680 dih5 -36.705 oc6 1.462958 occ6 108.324 dih6 6.139 nzn7 2.152409 nzno7 132.081 dih7 64.158 nzn8 2.114481 nzno8 107.602 dih8 -89.898 oo9 2.642453 ooc9 106.882 dih9 -125.536 co10 1.322791 coo10 107.006 dih10 4.699 oc11 1.268897 oco11 123.832 dih11 -1.681 oo12 2.501609 ooc12 140.105 dih12 -122.528 hc13 1.097938 hcc13 118.868 dih13 -174.525 hc14 1.098711 hco14 111.265 dih14 -128.639 ho15 1.025509 hoc15 109.353 dih15 -136.694 hn16 1.024370 hnzn16 111.555 dih16 43.641 hn17 1.023575 hnzn17 114.909 dih17 167.759 hn18 1.025503 hnzn18 103.070 dih18 -73.066 hn19 1.046183 hnzn19 103.393 dih19 -65.238 hn20 1.023705 hnzn20 115.615 dih20 175.011 hn21 1.024407 hnzn21 110.644 dih21 51.840 hn22 1.023079 hnzn22 117.378 dih22 -159.146 hn23 1.024543 hnzn23 109.219 dih23 -34.983 hn24 1.046418 hnzn24 102.526 dih24 80.720 hc25 1.136371 hco25 106.356 dih25 114.097 hc26 1.099887 hco26 116.246 dih26 178.275 ho27 1.030628 hoo27 12.823 dih27 -69.988 ho28 0.974450 hoo28 125.994 dih28 -69.803 Zn 0 LanL2DZ **** O 0 6-31G(d,p) **** N 0 6-31G(d,p) **** C 0 6-31G(d,p) **** H 0 6-31G(d,p) **** Geometry generated during the optimisation (with lower energy than the initial one): 28 6 -1.464949 1.509674 0.644918 6 -0.752663 1.944697 -0.538853 8 0.207081 1.232060 -0.900601 30 0.679807 -0.033321 0.002879 7 0.976977 -0.020466 0.650737 8 -0.540457 0.620465 0.863115 7 1.638350 0.213334 -0.532927 7 0.224412 -0.759996 -0.410095 8 -0.760249 -1.351593 0.255908 6 -1.860851 -1.501725 -0.398103 8 -2.755529 -0.648632 -0.176769 8 1.521317 -0.691880 0.408477 1 -1.080337 2.782444 -1.127697 1 -1.584411 2.285970 1.408241 1 -0.853265 -0.189964 1.143367 1 1.296370 0.599345 0.531586 1 2.344582 -0.529723 -0.772555 1 0.795747 0.255081 -1.150680 1 -0.085536 -1.254651 -0.689875 1 1.033419 -0.803980 -0.854007 1 -0.352758 0.145034 -0.591132 1 1.277134 -0.075128 0.947508 1 0.676202 0.896983 0.388030 1 0.733003 -0.394049 1.074588 1 -2.483655 0.979065 0.536577 1 -1.969773 -2.345455 -1.090252 1 0.723282 -1.280511 0.198896 1 2.351090 -1.100173 0.158205 From owner-chemistry@ccl.net Thu Jul 14 13:07:11 2005 From: "CCL" To: CCL Subject: CCL: g03 does not calculate frequencies Message-Id: <-28890-050714125515-24172-gJKokDZHWSap5rm98+rrIw-#-server.ccl.net> X-Original-From: "Crous Werner " Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C58894.CB7E67C0" MIME-Version: 1.0 Sent to CCL by: "Crous Werner " This is a multi-part message in MIME format. ------_=_NextPart_001_01C58894.CB7E67C0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Dear CCL =20 I was trying to modify parameters of the UFF-forcefield in Gaussian. The program gives the following error when I try to do an opt freq job: =20 There are 3 entries in the MM symbol table. Symbol 1 IAtTpT=3D 0 IUser=3D 0 String=3D* Symbol 2 IAtTpT=3D 10091000 IUser=3D 0 String=3DF_ Symbol 3 IAtTpT=3D 10011000 IUser=3D 0 String=3DH_ Number out of range in CpMMST. Error termination via Lnk1e in /opt/g03/l101.exe at Thu Jul 14 09:41:21 2005. =20 The optimization works fine, but g03 does not calculate the frequencies. Do somebody know what I am doing wrong or how I can fix this problem? Why is the number out of range? =20 Regards Werner =20 ------_=_NextPart_001_01C58894.CB7E67C0 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Dear CCL

 

I was trying to modify parameters of the = UFF-forcefield in Gaussian. The program gives the following error when I try to do an opt = freq job:

 

There are    3 entries in the MM symbol = table.

 Symbol    1 IAtTpT=3D           = 0 IUser=3D           0 String=3D*

 Symbol    2 IAtTpT=3D    10091000 = IUser=3D           0 String=3DF_

 Symbol    3 IAtTpT=3D    10011000 = IUser=3D           0 String=3DH_

 Number out of range in CpMMST.

 Error termination via Lnk1e in /opt/g03/l101.exe at Thu Jul 14 = 09:41:21 2005.

 

The optimization works fine, but g03 does not = calculate the frequencies. Do somebody know what I am doing wrong or how I can fix = this problem? Why is the number out of range?

 

Regards

Werner

 

------_=_NextPart_001_01C58894.CB7E67C0-- From owner-chemistry@ccl.net Thu Jul 14 13:26:05 2005 From: "CCL" To: CCL Subject: CCL: cart to zmatrix Message-Id: <-28891-050713141429-16905-gJKokDZHWSap5rm98+rrIw a server.ccl.net> X-Original-From: "PeeKay Emeye" Content-type: multipart/alternative; boundary="Next_1121274947---0-202.54.124.145-24138" MIME-Version: 1.0 Sent to CCL by: "PeeKay Emeye" This is a multipart mime message --Next_1121274947---0-202.54.124.145-24138 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline =A0=0ADear CCLers,=0Agreetings,=0A Can anybody tell me a way to conver ca= rtesian coordinate to zmatrix. Of course, the reverse is possible with Che= mcraft, thankfully.=0AThanking in advance=0AI remain=0AImran --Next_1121274947---0-202.54.124.145-24138 Content-type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline

=0A 
=0ADear CCLers,
=0Agreetings,
=0A     = ;Can anybody tell me a way to conver  cartesian coordinate to zmatrix.=   Of course, the reverse is possible with Chemcraft, thankfully.
= =0AThanking in advance
=0AI remain
=0AImran=0A

=0A

=0A= =0A --Next_1121274947---0-202.54.124.145-24138-- From owner-chemistry@ccl.net Thu Jul 14 16:58:59 2005 From: "CCL" To: CCL Subject: CCL: Gaussian 03, Opt. Changing ''maximum allowed number of steps''. Message-Id: <-28892-050714161716-7126-gJKokDZHWSap5rm98+rrIw]^[server.ccl.net> X-Original-From: "Niels Johan Christensen" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" MIME-Version: 1.0 Sent to CCL by: "Niels Johan Christensen" Dear All. When performing a (partial) geometry optimisation in G03, I would expect that POpt=MaxCycle=300 would set the maximum allowed number of optimisation steps to 300. However, when I inspect my .log file, I find the following line: Number of steps in this run= 168 maximum allowed number of steps= 168. How do I change this ''maximum allowed number of steps'' variable ? Thanks in advance. Yours sincerely, Niels Johan Christensen