Hi Thomas, Thanks for the report. Could you send me file "~/.dynamics/NameOfMolecule/log.txt". It contains every GROMACS output, so we will be able to analyse, what exactly GROMACS is missing.
You should also not remove those two lines of code. This is the part of code, which in case of such an error analyse "log.txt" file and create window on the screen, which contain useful information. Best regards, -- Tomasz Makarewicz, Laboratory of Biomolecular Systems Simulations, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland > Hi Tomasz, > > I quickly tested your plugin but wasn't able to run a similation. I have > gromacs 4.6.2 on Linux. This is what I got: > > Starting PyMOL plugin 'dynamics' ver. 2.0.0pre by Tomasz Makarewicz > updating project files > Calculating topology using Force fields > updating project files > Generating waterbox > Adding Water Box > updating project files > Energy Minimization > Unable to perform Energy Minimization > Fatal error: > There was 1 error in input file(s) > For more information and tips for troubleshooting, please check the > GROMACS > website at http://www.gromacs.org/Documentation/Errors > > Also on line 1078, I replaced Tk() by Toplevel() and dropped > root.mainloop() on line 1086 because that gave an error. > > Cheers, > Thomas > > Tomasz Makarewicz wrote, On 07/30/13 12:19: >> Dear PyMOL Users, >> >> I would like to announce you the plugin for PyMOL, which allows to >> perform >> molecular dynamics simulation on PyMOL loaded molecules using GROMACS >> and >> display results back to PyMOL in form of the animation. >> You can find more information on PyMOL Wiki: >> http://www.pymolwiki.org/index.php/GROMACS_Plugin >> and GitHub page of the project: >> https://github.com/tomaszmakarewicz/Dynamics >> The current work has been publish in scientific paper: >> http://pubs.acs.org/doi/abs/10.1021/ci400071x >> And you can find ready Ubuntu packages in following repository: >> https://launchpad.net/~tomaszm/+archive/dynamics >> >> If you have any question please do not hesitate to ask. >> >> In case of any bug, request or error please fill Issue on the GitHub >> page. >> >> Best regards, > > -- > Thomas Holder > PyMOL Developer > Schrödinger Contractor ----------------------------------------- Ten list został wysłany z serwera Uniwersytetu Gdańskiego. http://www.ug.edu.pl/ ------------------------------------------------------------------------------ Get your SQL database under version control now! Version control is standard for application code, but databases havent caught up. So what steps can you take to put your SQL databases under version control? Why should you start doing it? Read more to find out. http://pubads.g.doubleclick.net/gampad/clk?id=49501711&iu=/4140/ostg.clktrk _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
