From owner-chemistry@ccl.net Mon Dec 31 01:55:00 2007 From: "Shaillay Dogra shaillay/./strandls.com" To: CCL Subject: CCL: Substructure Search at QSARWorld Message-Id: <-35948-071231015005-24181-45+WiJ0bToPPJA+Uan16BA**server.ccl.net> X-Original-From: Shaillay Dogra Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Mon, 31 Dec 2007 12:17:00 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Shaillay Dogra [shaillay~~strandls.com] Hi, Now you can draw a structure and search for matching substructures in QSAR-World's 48 QSAR datasets. http://www.qsarworld.com/qsar-datasets-search.php Regards, Shaillay ----- Shaillay Kumar Dogra Scientific Editor (QSARWorld) http://www.qsarworld.com ---- From owner-chemistry@ccl.net Mon Dec 31 05:28:00 2007 From: "John Simmie john.simmie**nuigalway.ie" To: CCL Subject: CCL:G: Convergence of QCISD optimisation Message-Id: <-35949-071231051338-30163-v6lGafrV6RatJ+nivftnTA|a|server.ccl.net> X-Original-From: "John Simmie" Date: Mon, 31 Dec 2007 05:13:34 -0500 Sent to CCL by: "John Simmie" [john.simmie^^^nuigalway.ie] During a CBS-APNO composite calculation of a transition state with input: %nproc=8 %mem=16GB # CBS-APNO opt=(ts,noeigentest,calcfc,maxcycle=999) scf=qc ccsd=maxcyc=999 qcisd=conver=5 the first optimisation and the frequency calculation work fine but the second optimisation, which involves this computation #N Geom=AllCheck Guess=Read SCRF=Check QCISD/6-311G(d,p) Opt=RCFC takes forever and does not finish. See below Step Energy/kcal 1 0.56082406545 2 0.38311965015 3 0.68119293774 4 0.18504000137 5 0.53092323778 6 0.40429182067 7 0.00000000000 8 0.58391013994 9 0.38360283245 10 0.57052536231 11 0.48060952607 12 0.68359002401 13 1.04041075101 14 1.16339006282 15 1.23115481373 16 1.27288419548 17 1.34807238374 18 1.33770592682 19 1.31007040845 Is there a switch/keyword that I should be using to coax Gaussian-03 into finishing this phase and getting on with the five single-point energy determinations which are still to be done? From owner-chemistry@ccl.net Mon Dec 31 12:19:00 2007 From: "Ramachandrann chelat rcchelat(~)rediffmail.com" To: CCL Subject: CCL: Diagonal non-adiabatic corrections using Molpro Message-Id: <-35950-071231121614-1483-nI48yTErbUYtcbcbbuPJcQ_-_server.ccl.net> X-Original-From: "Ramachandrann chelat" Date: Mon, 31 Dec 2007 12:16:10 -0500 Sent to CCL by: "Ramachandrann chelat" [rcchelat|*|rediffmail.com] Dear CCL Friends, Few days back I had posted one doubt regarding the energy difference of some geometries of a HeH2^+ system using Molpro programs. The calculation were done using CASSCF method using cc-pV5Z basis set followed by MRCI calculations. However, I found an energy difference in the range of .0007 to .0009 hartrees. Later I found that the energy difference is because of the addition of a Diagonal non adiabatic correction to the previous value. The diagonal adiabatic corrections have added in the following way. A Full CI calculations have done using a smaller basis set (cc-PVTZ). This has been done by adding the nuclear kinetic energy operator to the adiabatic hamiltonian, the term like, G_alpha_alpha = , where X represents the nuclear coordinate, Phi_alpha the adiabatic wavefunction. The total diagonal non-adiabatic corrections to the ground state potential energies has been obtained by summing -1/2M * G_alpha_alpha terms(M is the atomica masse) over all of atoms. Can anyone of you help me to find out the Diagonal non-adiabatic corrections by this way using molpro programs? Can I get the correction directly from molpro output? Thanks in advance Ramachandran rcchelat-.-rediffmail.com From owner-chemistry@ccl.net Mon Dec 31 14:30:00 2007 From: "Jeff Nauss jnauss _ accelrys.com" To: CCL Subject: CCL: Accelrys Customer Training for January and February 2008 Message-Id: <-35951-071231142301-849-GIGYuCzkC9DeCGTO9S4Nrw###server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Mon, 31 Dec 2007 10:32:58 -0800 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss:-:accelrys.com] Accelrys Inc. are holding the following training workshops during January and February 2008. These events are designed to help you get more value > from your Accelrys software, helping you to better accomplish your research goals. Note that there will be a series of classroom sessions in India. Please contact our Bangalore office for registration and payment information for these special live sessions. Costs for on-line presentations is $175 per three hour session for all customers. On-line Sessions January 2008 Solvation Models in CHARMm 9 January (8am PST) InsightII to Discovery Studio Migration 10 January (8am PST) Catalyst to Discovery Studio Migration 11 January (8am PST) Introduction to Discovery Studio 14 January (8am PST) Sequence Analysis for Homology Modeling 15 January (8am PST) Protein Homology Modeling in Discovery Studio 16 January (8am PST) Simulations in Discovery Studio (Parts 1 & 2) 17-18 January (8am PST) Introduction to Material Studio 21 January (4pm GMT) Docking & Scoring in Discovery Studio 21 January (8am PST) De Novo Design with Discovery Studio 22 January (8am PST) Scripting in Materials Studio 22 January (4pm GMT) Pharmacophore Modeling in Discovery Studio 23-24 January (8am PST) On-line Sessions February 2008 InsightII to Discovery Studio Migration 4 February (8am PST) Catalyst to Discovery Studio Migration 5 February (8am PST) Introduction to Discovery Studio 11 February (8am PST) Sequence Analysis for Homology Modeling 12 February (8am PST) Protein Homology Modeling in Discovery Studio 13 February (8am PST) Simulations in Discovery Studio 14 - 15 February (8am PST) Docking & Scoring in Discovery Studio 18 February (8am PST) De Novo Design with Discovery Studio 19 February (8am PST) Pharmacophore Modeling in Discovery Studio 20 - 21 February (8am PST) India Classroom Sessions Contact our Bangalore office (http://www.accelrys.com/about/locations/bangalore.html) for further details. Delhi, Dr. B.R. Ambedkar Centre for Biomedical Research (ACBR) Introduction to Discovery Studio 28 January Docking & Scoring in Discovery Studio 29 January Hyderabad, University of Hyderabad Introduction to Discovery Studio 31 January Protein Homology Modeling in Discovery Studio 1 February Chennai, Sai's Biosciences Research Institute Private Ltd Introduction to Discovery Studio 4 February Protein Homology Modeling in Discovery Studio 5 February Mumbai, Dr. D. Y. Patil Institute of Bioinformatics & Biotechnology Introduction to Discovery Studio 7 February Docking & Scoring in Discovery Studio 8 February Further details for all training events can be found on our website at http://www.accelrys.com/services/training/general/calendar.html. Questions regarding scheduling and content should be directed to workshops,,accelrys.com. Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/services/training/ From owner-chemistry@ccl.net Mon Dec 31 21:48:01 2007 From: "Deepangi Pandit deepangi.pandit .. gmail.com" To: CCL Subject: CCL: Software to Create Schematic Diagram Message-Id: <-35952-071231181247-3136-i369Gg0BacCxsPJ1hK1QNw]=[server.ccl.net> X-Original-From: "Deepangi Pandit" Content-Type: multipart/alternative; boundary="----=_Part_5298_30430635.1199139475875" Date: Mon, 31 Dec 2007 17:17:55 -0500 MIME-Version: 1.0 Sent to CCL by: "Deepangi Pandit" [deepangi.pandit-#-gmail.com] ------=_Part_5298_30430635.1199139475875 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi: I find schematic diagrams/figures published in Nature Reviews of Drug Discovery(and similar publications) informative and useful. However, I do not know how could I create my own schematic diagrams to explain biological interactions like protein-ligand interactions, neurotransmitter interaction etc. I would like to know which commercial or free software could be used for these purposes. Thank you. Deepangi ------=_Part_5298_30430635.1199139475875 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi:
I find schematic diagrams/figures published in Nature Reviews of Drug Discovery(and similar publications) informative and useful. However, I do not know how could I create my own  schematic diagrams to explain biological interactions like protein-ligand interactions, neurotransmitter interaction etc. I would like to know which commercial or free software could be used for these purposes.
 
Thank you.
Deepangi
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