Thanks Sir for your quick response. These are the errors I am getting. Error in user input: Invalid command-line options In command-line option -f File '/home/Downloads/Free_Energy/MDP/EM/em_steep_0.mdp' does not exist or is not accessible. In command-line option -c File '/home/Downloads/Free_Energy/Methane/methane_water.gro' does not exist or is not accessible. In command-line option -p File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist or is not accessible. job.sh: line 30: mdrun: command not found
Error in user input: Invalid command-line options In command-line option -f File '/home/Downloads/Free_Energy/MDP/NVT/nvt_0.mdp' does not exist or is not accessible. In command-line option -p File '/home/Downloads/Free_Energy/Methane/topol.top' does not exist or is not accessible. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- job.sh: line 65: mdrun: command not found similar errors I get for all the sets. Regards Neelam Wafa On Mon, Apr 9, 2018 at 3:30 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 4/9/18 11:25 AM, neelam wafa wrote: > >> Dear sir Justin >> >> I am doing your tutorial of free energy calculations for methane in water. >> I have created the .mdp and .sh files using the perl script you >> provided. >> I have also made the FREE_ENERGY and MDP directories as in the job. sh >> script. gro file and topology files are also in the relevant folder but >> when I run job.sh script with command bash job.sh, it says the files the >> .mdp file, the methane_water.gro file and topol.top file either dont exist >> or not accessible. I have checked the files are in their proper places and >> are searched on terminal and opened though comand with vi editor. I have >> also given chmod 777 permission to these files. but no way out of the >> problem. please help me out. I have been searching the archive and google >> for the last three days but could not sort out. When i run the grompp and >> gmx md run commands directly through the terminal it works but not through >> the job.sh. >> Please suggest me a solution. Sorry for the long text or for addressing >> directly to you. >> > > Without specific error messages, I have nothing to go on to suggest a > solution. Perhaps you should be consulting your system administrator if the > commands are syntactically valid but not operational in the queued > environment. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.