[gmx-users] problem in running job.sh for free energy calculations.

[neelam wafa]

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 <jalemkul at 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
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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>
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