Schrödinger

Schrodinger [2] is a suite that is aimed to help the drug screening process (energy minimization, ligand-protein docking, building fragments, molecular dynamics, and so on). It is a widely-used application in the drug industries and in biomedical schools.

Important Notes

• License: Schrodinger's license is based on tokens which are reserved when you run jobs with multiple sub jobs. If you are planning to use Schrodinger, please contact hpc-supportATcase.edu to discuss  getting the permission, to talk about the restrictions or if you need to use more than 2 tokens. Also, see the section "License Management" below.

• It is a visual intensive Software and you are recommended to use X2Go or MobaXterm client (visit HPC GUI Access for instructions)

  • For lengthy jobs, we recommend running Schrodinger jobs either in batch mode, or REMOTELY (see Remote section below) to avoid job being halted by broken X-connection.

Installed Versions

All the available versions of SCHRODINGER for use on Rider can be viewed by issuing the following command. This applies for other applications as well.

$ module spider schrodinger

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  schrodinger: schrodinger/2017-3

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    Description:

      Schrodinger Suite for Drug Diiscovery

     Other possible modules matches:

        .base/schrodinger

    This module can be loaded directly: module load schrodinger/2017-3

The module can be loaded as:

module load schrodinger

The other versions of SCHRODINGER (when available) can be loaded as:

module load schrodinger/<version>

Running Schrodinger in HPC

Interactive Job

Serial:

Access compute node via x2go Client (visit HPC GUI Access for instructions). In the terminal type the following to get the compute node:

srun --x11 -N 1 -n 1 --time=10:00:00 --pty /bin/bash

You may want to request the time other than the default time of 10 hrs (--time=10:00:00) if your job takes longer to complete.

Load the module 

module load schrodinger

Run schrodinger's interface program:

maestro &

Parallel:

In Schrodinger, parallel jobs may be distributed over multiple cpus according to task division, or by data division. Task division applies for glide and for jaguar. Data division is the approach to run ligprep in parallel. Please search the Schrodinger documentation to determine how other packages within Schrodinger achieve parallel computation.

For task parallel jobs, allocate multiple tasks with -n <n>, where n is the number of processors. In this example, 4 processors (-n 4) are requested.

srun --x11 -N 1 -n 4 --time=10:00:00 --mem=20000MB --pty /bin/bash

You may want to assign enough memory (consider 4000MB/cpu) for your job to avoid unexpected termination due to "out of memory".

For data parallel jobs, allocate one task (-n 1) and then multiple processors using --cpus-per-task=<num cpus>. 

srun --x11 -N 1 -n 1 --cpus-per-task=4 --time=10:00:00 --mem=20000MB --pty /bin/bash

An example command for ligprep follows as created in a shell script [credit S. Kahremany]:

"${SCHRODINGER}"/utilities/para_ligprep -inp ligprep_test.inp -LOCAL -HOST "localhost:4" -NJOBS 20

Load the module and run maestro as in serial section above.

License Management

Please refer to HPC Software License Status.

Remote Schrodinger from PC

Run schrodinger from your PC using the Schrodigner license managed in HPC. Note that if your PC is linked to your own schrodinger license, you may want to disable it before using HPC schrodinger license.

Download Schrodinger (use version 2017-3 or earlier for compatibility)

Download Schrodinger from http://www.schrodinger.com/ -> Resources & Downloads -> Download. You may be asked to create a free account if you don't have it already. Choose the one that matches your platform (Linux/Windows/MAC). Also, make sure that you are downloading the version NOT newer than whatever is installed in HPC in case you want to use HPC Schrodinger license.

Install and configure Schrodinger

Note that the information on installation and configuration of schrodinger in  this link may contain stale information. So, always check the most recent environment variables for schrodinger by typing:

module display schrodinger

output: 

------------------------------------------------------------------------------------------

   /usr/local/share/modulefiles/Core/schrodinger/2017-3.lua:

------------------------------------------------------------------------------------------

whatis("Name: schrodinger")

whatis("Version 2017-3")

whatis("Category: library, software")

whatis("Description: Schrodinger Suite for Drug  Diiscovery")

pushenv("SCHRODINGER","/usr/local/schrodinger/2017-3")

pushenv("SCHRODINGER_THIRDPARTY","/usr/local/schrodinger/2017-3/thirdparty")

pushenv("SCHRODINGER_SQLITE_TEMP_STORE_DIRECTORY","/scratch/pbsjobs/schrodinger")

pushenv("MAESTRO_TEMP","/scratch/pbsjobs/schrodinger")

pushenv("MAESTRO_TEMP_LOCATION","/scratch/pbsjobs/schrodinger")

pushenv("SCHRODINGER_TEMP_PROJECT","/scratch/pbsjobs/schrodinger")

pushenv("SCHROD_LICENSE_FILE","27008@hpcmaster.case.edu")

pushenv("SCHROD_LIC","/usr/local/schrodinger/2017-3/mmshare-v3.9/bin/Linux-x86_64/lmutil lmstat -a -c 27008@hpcmaster")

prepend_path("LD_LIBRARY_PATH","/usr/local/schrodinger/2017-3/maestro-v11.3/lib/Linux-x86_64/gl")

prepend_path("PATH","/usr/local/schrodinger/2017-3")

Note the Schrodinger Path as /usr/local/schrodinger/2017-3 and license path as 27008@hpcmaster.case.edu.

Refer to HPC Guide to Molecular Modeling and Visualization and HPC Software Guide for more information.