From owner-chemistry@ccl.net Wed May 30 10:29:01 2018 From: "Kristyna Kantnerova kristyna.kantnerova/a\empa.ch" To: CCL Subject: CCL:G: Gaussian - ONIOM error Message-Id: <-53330-180530034747-25725-OxIw+I/G7JoWLAjn+HKhbA- -server.ccl.net> X-Original-From: "Kristyna Kantnerova" Date: Wed, 30 May 2018 03:47:43 -0400 Sent to CCL by: "Kristyna Kantnerova" [kristyna.kantnerova*empa.ch] Hi everyone, I prepared a Gaussian input file for an ONIOM calculation from a *.pdb file, in the software VMD using the molUP plugin. However, when I submit the job, it terminates with an error: Error parsing secondary structure: QPErr --- A syntax error was detected in the input line. N O C H 0 ' Last state= "Top" TCursr= 101 LCursr= 0 I didn't find any similar error on Google, would someone please know what is missing in the input file? Many thanks! **** extract of the input file ***** %chk=kan_oniom01.chk %nprocshared=24 %mem=8192MB # ONIOM(B3LYP/GenECP:Amber=hardfirst) 5d geom=connectivity First ONIOM 0 1 0 1 0 1 N-N-0.000000(PDBName=N,ResName=PHE,ResNum=10) 0 32.381001 51.759998 44.515999 L C-CA-0.000000(PDBName=CA,ResName=PHE,ResNum=10) 0 33.618999 51.000999 44.867001 L C-C-0.000000(PDBName=C,ResName=PHE,ResNum=10) 0 34.473000 50.556000 43.678001 L O-O-0.000000(PDBName=O,ResName=PHE,ResNum=10) 0 33.967999 49.882999 42.764999 L C-CB-0.000000(PDBName=CB,ResName=PHE,ResNum=10) 0 33.257000 49.764000 45.672001 L ...(lines left out).... N-N-0.000000(PDBName=N,ResName=HEM,ResNum=802) 0 18.964001 17.402000 38.542999 H O-O-0.000000(PDBName=O,ResName=HEM,ResNum=802) 0 18.048519 16.814085 39.545734 H N-N-0.000000(PDBName=N,ResName=HEM,ResNum=802) 0 20.209387 17.594355 38.998669 H O-O-0.000000(PDBName=O,ResName=FE,ResNum=803) 0 20.460312 17.172688 40.469860 H 1 2 1.0 2 3 1.0 12 1.0 5 1.0 3 20 1.0 4 1.0 4 5 6 1.0 14 1.0 13 1.0 ...(lines left out).... 9636 9637 1.0 9638 1.0 9637 9638 9639 1.0 9639 N O C H 0 6-31g** **** Fe 0 LANL2dz **** Fe 0 LANL2dz **** end of the input file**** P.S. I noticed that ONIOM files have at some rows also a reference on the linking atoms, like that (H-HC-0.1 5): C-CA--0.25 0 -5.419886 -0.619477 -0.778859 L H-HC-0.1 5 This is missing in my input file, I have there just the list of atoms without this additional info at some rows. Could that be the problem? How should I include it there, in case it is needed? I would expect the molUP plugin in VMD would do this for me automatically, as its main purpose actually is to prepare ONIOM input files. Thank you! From owner-chemistry@ccl.net Wed May 30 11:04:00 2018 From: "Thomas Exner thomas.exner:_:uni-konstanz.de" To: CCL Subject: CCL: Additional eChemInfo workshop on drug design in Oxford,. UK Message-Id: <-53331-180530055819-8484-fP2ARbDalyuVwuscDc1M5Q||server.ccl.net> X-Original-From: Thomas Exner Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Wed, 30 May 2018 11:58:02 +0200 MIME-Version: 1.0 Sent to CCL by: Thomas Exner [thomas.exner+*+uni-konstanz.de] Dear CCLers: This is the first announcement for an additional eChemInfo Training and Innovation Course in Drug Design 3-7 September 2018 Diamond House, Harwell Science & Innovation Campus Details and preliminary program are available at http://www.echeminfo.com/events/echeminfo-oxford-2018. Deadline for bursary applications and early-bird reduced registration rates is August 1. Hope to see you there. Thomas P.S.: And you have still one day to profit for the Milano early-bird rates. Thomas Exner schrieb: > Dear all: > > Just a quick note that you can still profit from the early bird rates > until the extended deadline May 31. > > Best. > Thomas > >   Thomas Exner thomas.exner##douglasconnect.com schrieb: >> Sent to CCL by: "Thomas  Exner" [thomas.exner]_[douglasconnect.com] >> Continuation of our workshop to resolve your problems in drug design >> >> Training and Innovation Course in Drug Design >> 17-21 July 2018 >> Department of Pharmaceutical Sciences, University of Milan >> >> Bring your own problems in rational drug design to this hands-on >> workshop co-organized by the University of Milans Department of >> Pharmaceutical Sciences and eChemInfo. >> >> Over one week, top modeling experts will teach you >> state-of-the-art/emerging approaches and tools and help you apply new >> knowledge to your own research. >> >> Real-world examples from academia and industry, as well as >> experimental techniques, will be strongly integrated into the >> workshop. Get personalized advice from Stefano Moro, University of >> Padova, working on G protein-coupled receptor ligand recognition >> pathways; Anthony Bradley from the Diamond Light Source's XChem >> project providing services for complex structure determination using >> medium- to high-throughput X-ray; and other industry experts soon to >> be announced. >> >> Participants - chemists, life scientists and modellers working in >> rational drug design - will return to their labs with new ideas, best >> practices and software experiences to maximise productivity in their >> own drug discovery research activities. >> >> http://www.echeminfo.com/events/echeminfo-euro-2018 >> >> The workshop will provide a set of stimulating lectures and group >> work sessions on: >> - virtual screening, >> - ligand-based and structure-based drug design, >> - bio- and cheminformatics, >> - molecular dynamics simulation, >> - drug delivery modelling, >> - off-target predictions and >> - quantum mechanics in the hit-to-lead phase >> >> The functionalities of tools developed in academic groups and from >> the main software providers will be explored based on tutorials and, >> even more important, on case studies taken from ongoing research. >> >> Posters are welcome to give the other attendees an overview of your >> work and foster discussion within the groups. >> >> Bursary Awards are available; deadline extended until 30 April at >> http://www.echeminfo.com/bursary-awards >> >> Early-bird reduced rates are also available until 30 April. >> >> For further information and questions on this (updated program, exact >> location, suggestions for accommodation,...) and other eChemInfo >> workshops, please visit http://www.echeminfo.com/events or contact us. >> Alessandro Contini, University of Milano (alessandro.contini%%unimi.it) >> Thomas Exner, Douglas Connect (thomas.exner%%douglasconnect.com) >> >> P.S.: Please spread the word by showcasing the attached poster on >> your notice boards.>>       >>       >>       >>       >> >> > > -- ___________________________________________________________________________________ Dr. Thomas E. Exner Chief Scientific Officer Douglas Connect GmbH. www: www.douglasconnect.com e-mail: thomas.exner-,-douglasconnect.com phone: +49 (0)171 3807485