FEP+ Web Services Command Line Tasks
- Linux
- Mac
- Windows
Use the "jws" command to manage FEP+ Web Services jobs. Each "jws" command consists of an "action", "flags" to specify additional options for that action, and in some cases, a "job identifier" to specify the job on which the action should be performed. You can use -jobid or -jobname as job identifiers. The examples below use -jobname.
Open a terminal to run commands.
To list all possible jws actions and display information about them, use the -h flag:
$SCHRODINGER/jws -h
To display usage information on a specific action, use the -h flag after that action:
$SCHRODINGER/jws [ACTION] -h
Listing Jobs
and displaying job information
To list jobs submitted by the user, use the following command:
$SCHRODINGER/jws list-jobs
This returns a table that lists information for jobs submitted:
project jobid jobname fep_type schrodinger_path status date submitted --------- -------- ------------ -------------- ------------------ -------- --------------------------- demo xxxxxxxx fep_mapper_1 small_molecule OB/2023-3/release finished 2023-07-30T19:07:52.477709Z
To list information about a specific job, use the following command:
$SCHRODINGER/jws info -jobname fep_mapper_1
Downloading trajectories
To download the fmp file of a job with trajectories, use the following command:
$SCHRODINGER/jws download-graph -jobname JOBNAME -basename BASENAME -with-trajectories
-basename specifies the destination path; the downloaded fmp file has the name <BASENAME>.fmp. -with-trajectories specifies that trajectories are also downloaded.
Generating and downloading custom force field parameters
To calculate force field parameters on the fly, make sure that the "Generate missing parameters with Force field builder" option is selected.
To download the force field parameters to a local tar archive (jws_download.tar.gz), use the following command:
$SCHRODINGER/jws download-forcefield -jobid <jobid>
You can run the following command to find the <jobid>:
$SCHRODINGER/jws list-jobs
Uncompress the jws_download.tar.gz to obtain the custom_<release version>.opls file (i.e. custom_2024_2.opls):
tar xvfz jws_download.tar.gz
To merge OPLS custom parameters, you can run the custom_params utility.
Extending the simulation time
To extend all edges in the graph by 5 ns, use the -graph option with the extend subcommand:
$SCHRODINGER/jws extend -jobname JOBNAME -graph
To extend a particular edge by 5 ns, use -edge ligand1 ligand2 with the extend subcommand, where ligand1 and ligand2 are the names of the ligands that make up the edge. The edge is extended from ligand1 to ligand2:
$SCHRODINGER/jws extend -jobname JOBNAME -edge ligand1 ligand2
To extend all edges directly attached to a ligand by 5 ns, use -node ligand with the extend subcommand, where ligand is the name of the ligand:
$SCHRODINGER/jws extend -jobname JOBNAME -node ligand
Show available credits
To show total, available, and used credits for a project, use the following command:
$SCHRODINGER/jws show-credits -project-name PROJECT_NAME
Add a user to a graph
You can give a user access to a job. Only the owner of the graph or users that have been added can add new users in the same project. For example, to give a user with username USER1 to the fep_mapper_1 job, use the following command:
$SCHRODINGER/jws add-user -jobname JOBNAME -username USER1
Use the "jws" command to manage FEP+ Web Services jobs. Each "jws" command consists of an "action", "flags" to specify additional options for that action, and in some cases, a "job identifier" to specify the job on which the action should be performed. You can use -jobid or -jobname as job identifiers. The examples below use -jobname.
Open a terminal to run commands.
To list all possible jws actions and display information about them, use the -h flag:
$SCHRODINGER/jws -h
To display usage information on a specific action, use the -h flag after that action:
$SCHRODINGER/jws [ACTION] -h
Listing Jobs
and displaying job information
To list jobs submitted by the user, use the following command:
$SCHRODINGER/jws list-jobs
This returns a table that lists information for jobs submitted:
project jobid jobname fep_type schrodinger_path status date submitted --------- -------- ------------ -------------- ------------------ -------- --------------------------- demo xxxxxxxx fep_mapper_1 small_molecule OB/2023-3/release finished 2023-07-30T19:07:52.477709Z
To list information about a specific job, use the following command:
$SCHRODINGER/jws info -jobname fep_mapper_1
Downloading trajectories
To download the fmp file of a job with trajectories, use the following command:
$SCHRODINGER/jws download-graph -jobname JOBNAME -basename BASENAME -with-trajectories
-basename specifies the destination path; the downloaded fmp file has the name <BASENAME>.fmp. -with-trajectories specifies that trajectories are also downloaded.
Generating and downloading custom force field parameters
To calculate force field parameters on the fly, make sure that the "Generate missing parameters with Force field builder" option is selected.
To download the force field parameters to a local tar archive (jws_download.tar.gz), use the following command:
$SCHRODINGER/jws download-forcefield -jobid <jobid>
You can run the following command to find the <jobid>:
$SCHRODINGER/jws list-jobs
Uncompress the jws_download.tar.gz to obtain the custom_<release version>.opls file (i.e. custom_2024_2.opls):
tar xvfz jws_download.tar.gz
To merge OPLS custom parameters, you can run the custom_params utility.
Extending the simulation time
To extend all edges in the graph by 5 ns, use the -graph option with the extend subcommand:
$SCHRODINGER/jws extend -jobname JOBNAME -graph
To extend a particular edge by 5 ns, use -edge ligand1 ligand2 with the extend subcommand, where ligand1 and ligand2 are the names of the ligands that make up the edge. The edge is extended from ligand1 to ligand2:
$SCHRODINGER/jws extend -jobname JOBNAME -edge ligand1 ligand2
To extend all edges directly attached to a ligand by 5 ns, use -node ligand with the extend subcommand, where ligand is the name of the ligand:
$SCHRODINGER/jws extend -jobname JOBNAME -node ligand
Show available credits
To show total, available, and used credits for a project, use the following command:
$SCHRODINGER/jws show-credits -project-name PROJECT_NAME
Add a user to a graph
You can give a user access to a job. Only the owner of the graph or users that have been added can add new users in the same project. For example, to give a user with username USER1 to the fep_mapper_1 job, use the following command:
$SCHRODINGER/jws add-user -jobname JOBNAME -username USER1
Use the "jws" command to manage FEP+ Web Services jobs. Each "jws" command consists of an "action", "flags" to specify additional options for that action, and in some cases, a "job identifier" to specify the job on which the action should be performed. You can use -jobid or -jobname as job identifiers. The examples below use -jobname.
To run commands, go to the start menu, open the currently installed version of the Schrodinger tools, and click on Schrodinger Command Prompt.
To list all possible jws actions and display information about them, use the -h flag:
jws -h
To display usage information on a specific action, use the -h flag after that action:
jws [ACTION] -h
Listing Jobs
and displaying job information
To list jobs submitted by the user, use the following command:
jws list-jobs
This returns a table that lists information for jobs submitted:
project jobid jobname fep_type schrodinger_path status date submitted --------- -------- ------------ -------------- ------------------ -------- --------------------------- demo xxxxxxxx fep_mapper_1 small_molecule OB/2023-3/release finished 2023-07-30T19:07:52.477709Z
To list information about a specific job, use the following command:
jws info -jobname fep_mapper_1
Downloading trajectories
To download the fmp file of a job with trajectories, use the following command:
jws download-graph -jobname JOBNAME -basename BASENAME -with-trajectories
-basename specifies the destination path; the downloaded fmp file has the name <BASENAME>.fmp. -with-trajectories specifies that trajectories are also downloaded.
Generating and downloading custom force field parameters
To calculate force field parameters on the fly, make sure that the "Generate missing parameters with Force field builder" option is selected.
To download the force field parameters to a local tar archive (jws_download.tar.gz), use the following command:
jws download-forcefield -jobid <jobid>
You can run the following command to find the <jobid>:
jws download-forcefield list-jobs
Uncompress the jws_download.tar.gz to obtain the custom_<release version>.opls file (i.e. custom_2024_2.opls):
tar xvfz jws_download.tar.gz
To merge OPLS custom parameters, you can run the custom_params utility.
Extending the simulation time
To extend all edges in the graph by 5 ns, use the -graph option with the extend subcommand:
jws extend -jobname JOBNAME -graph
To extend a particular edge by 5 ns, use -edge ligand1 ligand2 with the extend subcommand, where ligand1 and ligand2 are the names of the ligands that make up the edge. The edge is extended from ligand1 to ligand2:
jws extend -jobname JOBNAME -edge ligand1 ligand2
To extend all edges directly attached to a ligand by 5 ns, use -node ligand with the extend subcommand, where ligand is the name of the ligand:
jws extend -jobname JOBNAME -node ligand
Show available credits
To show total, available, and used credits for a project, use the following command:
jws show-credits -project-name PROJECT_NAME
Add a user to a graph
You can give a user access to a job. Only the owner of the graph or users that have been added can add new users in the same project. For example, to give a user with username USER1 to the fep_mapper_1 job, use the following command:
jws add-user -jobname JOBNAME -username USER1