From owner-chemistry@ccl.net Thu Nov 20 05:38:01 2014 From: "Sergio Manzetti sergio.manzetti%%outlook.com" To: CCL Subject: CCL: Nanotubes with Amber (GAFF) ff in GROMACS Message-Id: <-50764-141120053654-1333-849Rw5RI+rRObhDHX26I+Q ~~ server.ccl.net> X-Original-From: "Sergio Manzetti" Date: Thu, 20 Nov 2014 05:36:51 -0500 Sent to CCL by: "Sergio Manzetti" [sergio.manzetti_._outlook.com] Does anyone know of a tutorial that explains the procedure to generate non-periodic *gro, *top and *itp files for the GAFF force field in GROMACS 5.0+ ? Thanks! From owner-chemistry@ccl.net Thu Nov 20 13:50:01 2014 From: "Douglas Houston DouglasR.Houston,ed.ac.uk" To: CCL Subject: CCL:G: MOPAC cube file ..? Message-Id: <-50765-141120125326-30688-mECMlYkyoC3Qp/G0LhKn4Q**server.ccl.net> X-Original-From: Douglas Houston Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Thu, 20 Nov 2014 17:53:10 +0000 MIME-Version: 1.0 Sent to CCL by: Douglas Houston [DouglasR.Houston^ed.ac.uk] Thanks Chris & Christos. The AUX file idea tallies with what James Stewart suggested was the best format (because "The output files are liable to be changed at any time, this makes them unsuitable for use by other software"). However Jimmy was unable to tell me if the AUX format contained (an equivalent to) the volumetric data used in cube files. Presumably if the conversion occurs without error then it must? cheers, Doug Quoting "Christos Garoufalis garoufal .. physics.upatras.gr" on Wed, 19 Nov 2014 14:04:57 -0500: > > Sent to CCL by: "Christos Garoufalis" [garoufal_-_physics.upatras.gr] > If you run the mopac calculation with the "AUX" keyword > it will produce a *.aux file. > This file can be read by gabedit and converted to cube. > > > > >> "Douglas Houston DouglasR.Houston#ed.ac.uk" wrote: >> >> Sent to CCL by: Douglas Houston [DouglasR.Houston-x-ed.ac.uk] >> Hi all, >> >> Can anyone tell me if there is a way to convert from any of the output >> formats that MOPAC2012 can write to GAUSSIAN cube file format? >> >> Failing that, would it be possible to send me an example cube file for >> something simple like e.g. ethane? >> >> cheers, >> Doug >> >> _____________________________________________________ >> Dr. Douglas R. Houston >> Lecturer >> Institute of Structural and Molecular Biology >> Room 3.23, Michael Swann Building >> King's Buildings >> University of Edinburgh >> Edinburgh, EH9 3JR, UK >> Tel. 0131 650 7358 >> http://tinyurl.com/douglasrhouston >> >> -- >> The University of Edinburgh is a charitable body, registered in >> Scotland, with registration number SC005336.> > > > _____________________________________________________ Dr. Douglas R. Houston Lecturer Institute of Structural and Molecular Biology Room 3.23, Michael Swann Building King's Buildings University of Edinburgh Edinburgh, EH9 3JR, UK Tel. 0131 650 7358 http://tinyurl.com/douglasrhouston -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. From owner-chemistry@ccl.net Thu Nov 20 14:24:01 2014 From: "Jim Kress ccl_nospam]![kressworks.com" To: CCL Subject: CCL: Nanotubes with Amber (GAFF) ff in GROMACS Message-Id: <-50766-141120133128-9881-tz6Za7qc5/cjkIFR/eNj/A_+_server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 20 Nov 2014 13:31:21 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam * kressworks.com] I'd suggest you send that question to the gromacs list: Send gromacs.org_gmx-developers mailing list submissions to gromacs.org_gmx-developers^^maillist.sys.kth.se To subscribe or unsubscribe via the World Wide Web, visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-developers or, via email, send a message with subject or body 'help' to gromacs.org_gmx-developers-request^^maillist.sys.kth.se Jim -----Original Message----- > From: owner-chemistry+jimkress35==gmail.com^^ccl.net [mailto:owner-chemistry+jimkress35==gmail.com^^ccl.net] On Behalf Of Sergio Manzetti sergio.manzetti%%outlook.com Sent: Thursday, November 20, 2014 5:37 AM To: Kress, Jim Subject: CCL: Nanotubes with Amber (GAFF) ff in GROMACS Sent to CCL by: "Sergio Manzetti" [sergio.manzetti_._outlook.com] Does anyone know of a tutorial that explains the procedure to generate non-periodic *gro, *top and *itp files for the GAFF force field in GROMACS 5.0+ ? Thanks!http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Nov 20 16:14:01 2014 From: "Geoffrey Hutchison geoffh[-]pitt.edu" To: CCL Subject: CCL:G: MOPAC cube file ..? Message-Id: <-50767-141120143648-4660-2EDJULzJLg2FBYOH1oJFpA_-_server.ccl.net> X-Original-From: Geoffrey Hutchison Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 20 Nov 2014 14:36:32 -0500 Mime-Version: 1.0 (Mac OS X Mail 8.1 \(1993\)) Sent to CCL by: Geoffrey Hutchison [geoffh*pitt.edu] > However Jimmy was unable to tell me if the AUX format contained (an equivalent to) the volumetric data used in cube files. The MOPAC aux files are the equivalent to Gaussian .fchk files - that is, these files contain the MO coefficients, slater basis set, etc. Hope that helps, -Geoff --- Prof. Geoffrey Hutchison Department of Chemistry University of Pittsburgh tel: (412) 648-0492 email: geoffh^^pitt.edu web: http://hutchison.chem.pitt.edu/ From owner-chemistry@ccl.net Thu Nov 20 19:21:01 2014 From: "Christos Garoufalis garoufal%gmail.com" To: CCL Subject: CCL:G: MOPAC cube file ..? Message-Id: <-50768-141120162316-31806-zObqYkGma+9CT/zTLZeCTQ..server.ccl.net> X-Original-From: Christos Garoufalis Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 20 Nov 2014 23:22:36 +0200 MIME-Version: 1.0 Sent to CCL by: Christos Garoufalis [garoufal###gmail.com] Hi Doug, the *.aux file contains the eigenvectors, density matrix hessian etc. (not the volumetric data). However the file format is easily read by gabedit (http://gabedit.sourceforge.net/ ) which is free and can create/visualize/save all the the volumetric data you need. So it is just a matter of a few seconds to create cube the files you want. Christos On 20-Nov-14 7:53 PM, Douglas Houston DouglasR.Houston,ed.ac.uk wrote: > > Sent to CCL by: Douglas Houston [DouglasR.Houston^ed.ac.uk] > Thanks Chris & Christos. > > The AUX file idea tallies with what James Stewart suggested was the > best format (because "The output files are liable to be changed at any > time, this makes them unsuitable for use by other software"). > > However Jimmy was unable to tell me if the AUX format contained (an > equivalent to) the volumetric data used in cube files. > > Presumably if the conversion occurs without error then it must? > > cheers, > Doug > > > > Quoting "Christos Garoufalis garoufal .. physics.upatras.gr" > on Wed, 19 Nov 2014 14:04:57 -0500: > >> >> Sent to CCL by: "Christos Garoufalis" [garoufal_-_physics.upatras.gr] >> If you run the mopac calculation with the "AUX" keyword >> it will produce a *.aux file. >> This file can be read by gabedit and converted to cube. >> >> >> >> >>> "Douglas Houston DouglasR.Houston#ed.ac.uk" wrote: >>> >>> Sent to CCL by: Douglas Houston [DouglasR.Houston-x-ed.ac.uk] >>> Hi all, >>> >>> Can anyone tell me if there is a way to convert from any of the output >>> formats that MOPAC2012 can write to GAUSSIAN cube file format? >>> >>> Failing that, would it be possible to send me an example cube file for >>> something simple like e.g. ethane? >>> >>> cheers, >>> Doug >>> >>> _____________________________________________________ >>> Dr. Douglas R. Houston >>> Lecturer >>> Institute of Structural and Molecular Biology >>> Room 3.23, Michael Swann Building >>> King's Buildings >>> University of Edinburgh >>> Edinburgh, EH9 3JR, UK >>> Tel. 0131 650 7358 >>> http://tinyurl.com/douglasrhouston >>> >>> -- >>> The University of Edinburgh is a charitable body, registered in >>> Scotland, with registration number SC005336.> >> >> >> > > > > > _____________________________________________________ > Dr. Douglas R. Houston > Lecturer > Institute of Structural and Molecular Biology > Room 3.23, Michael Swann Building > King's Buildings > University of Edinburgh > Edinburgh, EH9 3JR, UK > Tel. 0131 650 7358 > http://tinyurl.com/douglasrhouston > From owner-chemistry@ccl.net Thu Nov 20 22:44:01 2014 From: "Mark Berger mark94025__comcast.net" To: CCL Subject: CCL: Reminder: NBCR AMBER Workshop - UCSD - Mon Dec 15th to Thur Dec 18th Message-Id: <-50769-141120212130-6364-r3qUKURJQRlj1qccjdqLvA!^!server.ccl.net> X-Original-From: "Mark Berger" Date: Thu, 20 Nov 2014 21:21:29 -0500 Sent to CCL by: "Mark Berger" [mark94025]~[comcast.net] Dear All, We are glad to announce that registration is open for the NBCR Amber Workshop 2014 that will be held at the faculty club of the University of California San Diego from the Mon 15th to Thur 18th Dec 2014. The course will be taught by Ross C. Walker and Rommie Amaro with additional instructors to be determined shortly. More info: http://nbcr.ucsd.edu/wordpress2/?page_id=4086 Please feel free to forward this announcement to all your contacts. With the best regards, The Organizing Team * Program The duration of the meeting is 4 days, from Dec 15th to 18th 2014. A provisional program is available on the workshop webpage (http://nbcr.ucsd.edu/wordpress2/?page_id=4086). Typically there will be lectures 3 to 4 hours per day, and hands-on tutorials, about 4 hours per day. There will also be 2 or 3 guest research lectures from local faculty as well as a poster session in which attendees will have the opportunity to present their work and engage directly with developers of the AMBER software. Thanks to sponsorship from NVIDIA a K40 GPU will be given as a poster prize. The content of the Workshop will include: * Molecular Dynamics with Amber * Using VMD to visualize AMBER * Dealing with non-standard residues * Building protein-ligand complexes * Statistical Mechanics for Free Energy Calculations * MM/PBSA calculations * Thermodynamic Integration * Enhanced sampling techniques * Markov State Models with AMBER * Accelerated Molecular Dynamics * Using the Kepler Bioworkbench - Workflows for AMBER * Analyzing Simulations * Lipid Simulations with AMBER The target audience is graduate students and postdocs as well as a few faculty interested in learning about Molecular Dynamics techniques. The course is designed to introduce Molecular Dynamics techniques from an introductory perspective but will progress quickly. Some experience with the Linux operating system is essential but experience with AMBER or other molecular dynamics packages is not required. * Registration Registration is limited to 40 participants. The registration fee is $350 and includes a USB drive for all participants containing lecture notes, hands on tutorials and a Virtual Box image with all software used in the workshop; Coffee, snacks and refreshments on all 4 days; A buffet lunch on all 4 days; a poster session and social reception and a workshop dinner. To register please visit the following page: http://nbcr.ucsd.edu/wordpress2/?page_id=4086 Important: Registration deadline is December 1st 2014. Hotels in San Diego at this time of year are likely to fill up fast so we recommend you make arrangements soon. Information regarding finding roommates to share hotel rooms will be available during registration. Attendees are expected to bring their own laptop. The organization will provide a pen-drive with all necessary software and training material.