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Schrodinger

Schrodinger

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  to discuss about 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 NX Client (visit HPC GUI Access for instructions)
  • To run Schrodinger jobs from the compute nodes, you are importing the graphic environment of Schrodinger to your local terminal. Since this requires a lot of connection bandwidth, please use wired campus connection for best usage.
  • We recommend running Schrodinger job REMOTELY (see Remote section below) to avoid job being halted by broken X-connection.

Installed Versions

All the available versions of SCHRODINGER for use can be viewed by issuing the following command. This applies for other applications as well.
module avail schrodinger
output:
---------------------- /usr/local/share/modulefiles -------------------------
schrodinger/2015-3 (D)

The default version is identified by "(D)" behind the module name and can be loaded as:
module load schrodinger

The other versions of SCHRODINGER can be loaded as:
module load schrodinger/<version>

Running Schrodinger in HPC

Interactive Job

Serial:
Access compute node via NX Client (visit HPC GUI Access for instructions). In the terminla type the following to get the compute node:
srun --x11 -N 1 -c 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:
For parallel job, you need to assign multiple processors with -c <n>, where n is the number of processors. In this example, 4 processors (-c 4) are requested.
srun --x11 -N 1 -c 4 --time=10:00:00 --mem=5gb --pty /bin/bash
You may want to assign enough memory (--mem=5gb) for your job to avoid unexpected termination due to "out of memory".

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

License Management

Remote Schrodinger from PC

It allows you to 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

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/schrodinger/2015-3:
----------------------------------------------------------------------------
whatis("Loads Schrodinger 2015-3 ")
setenv("SCHRODINGER","/usr/local/schrodinger/2015-3")
setenv("SCHRODINGER_THIRDPARTY","/usr/local/schrodinger/2015-3/thirdparty")
setenv("SCHRODINGER_SQLITE_TEMP_STORE_DIRECTORY","/tmp")
setenv("MAESTRO_TEMP","/tmp")
setenv("MAESTRO_TEMP_LOCATION","/tmp")
setenv("SCHRODINGER_TEMP_PROJECT","/tmp")
setenv("SCHROD_LICENSE_FILE","27008@hpcmaster.case.edu")
prepend_path("PATH","/usr/local/schrodinger/2015-3")

Note the Schrodinger Path as /usr/local/schrodinger/2015-3 and license path as 27008@hpcmaster.case.edu.

Older Info:
Please follow instructions on the following handouts for Windows, and Linux/Mac

For more insight, some of the steps are outlined here too but look out for outdated information.
  • You have to download the software first from hpclogin: /usr/local/doc/schrodinger/... (the appropriate version for your desktop); use of the utilities explained here or you can use Globus Online. You can also download it directly from Schrodinger website (schrodinger.com). Please download all the tools that you need.
    (Please contact the cluster admin should you have transfer issues)

  • Install the software on your local desktop: Run the executable that you downloaded.

  • You may need to have OpenGL installed if you use Linux. OpenGL is already installed in Windows.

  • Set SCHROD_LICENSE_FILE to 27008@hpcmaster.case.edu
    • In the Windows environment (Right click on My Computer -> Properties -> Advanced tab -> Environment Variables button at the bottom -> Edit user variable -> Save/OK. (thanks Matthew Kalp)
    • or put EXPORT SCHROD_LICENSE_FILE=27008@hpcmaster.case.edu in the .bashrc on your desktop in Linux

  • Set the ssh-without-password from to the cluster. You can use Putty or SSH setup
  • Add the cluster information in the schrodinger.hosts file. This will add the cluster as an option to run your Schrodinger jobs.
    An example of this file is given in this link

  • Open Maestro (use "maestro -SGL" in Linux to link to the OpenGL library)

  • Pick the cluster option (HPC) to run your job in the HPC environment
Please follow instructions on the following handouts for Windows, and Linux
(! You will need to replace arc-login with hpcmaster in the above handouts)

RUN

  • Open Maestro Window: Start->All Programs->Schrodinger2010->maestro 9.1
  • Open the tutorial: Help->Manual Index and find Maestro Tutorial under Section Maestro 9.1

Desmond

The desmond package is installed in hpctest (SLURM cluster).

module load schrodinger
which desmond
output:
/usr/local/schrodinger/2015-3/desmond

This Desmond Guide can be helpful.

Troubleshooting

For more troubleshooting info refer to Schrodinger KB [3].

Problem: When attempting to edit the schrodinger.hosts file for remote host, I received the message "Access denied."
Solution: change the permission so that you have the edit permission. In Linix/Mac, use chmod 644 schrodinger.hosts and in windows, right click on the schrodinger.hosts file, and you'll see 'properties' at the bottom of the pop-up. Select that, and you should be able to change the permissions to allow your user account to write in that file.

References:

[1] Schrodinger FAQ: https://www.schrodinger.com/supportfaq/18/
[2] Schrodinger website: https://www.schrodinger.com/