====== Schrodinger at CHPC ======

This is a package provided by [[https://www.schrodinger.com/|SCHRODINGER]]

This license can only be used by CHPC registered users, which are associated with **South African** higher education institutions

To gain access to Schrodinger you need to contact us via HelpDesk page [[https://users.chpc.ac.za/helpdesk]] or via email to helpdesk@chpc.ac.za   If we have we have approved you for usage of the software, this page will be helpful to you:     [[approved schrodinger users]]

We can then ensure that you get added to the appropriate group and will then provide you with the installation files and instructions needed to setup the software on your laptop or desktop.

You will need to **edit your "//hosts.//" file** (with no extension). The edit is done by copying this //hosts// file to one of your own dirs such as Documents, edit there, and then copy file back (in the etc\ dir you can't easily edit directly). Do the copy as Administrator (and using Admin elsewhere may help too).

**Please make sure you add the following line** in the C:\Windows\System32\drivers\etc\hosts file

//10.128.15.123 mslogin.chpc.ac.za mslogin//

**Remove** any other line such as.

196.24.44.123 mslogin.chpc.ac.za mslogin

The current Schrödinger installation differs slightly from the **original guide**. Please also refer to the **document below** in addition to the **original installation instructions**.

{{ :howto:new-schrodinger-install-guide.pdf |}}

**Configure Passwordless SSH for Schrödinger Job Control**

Important: Before submitting Schrödinger jobs using the qschrodinger_* scripts, ensure that passwordless SSH is configured for internal communication between the login and compute nodes. This is required by Schrödinger Job Control for launching and managing jobs.

**Setting up Internal ssh key** 

1.Navigate to your SSH directory:
   cd ~/.ssh

2.List the contents to verify your SSH keys:
   ls -l

3.If you see the cluster-generated keys (id_hpc_mpi and id_hpc_mpi.pub), use those. Otherwise, if you have generated an ECDSA key, use id_ecdsa.pub.
 
4.Check whether your public key is already in authorized_keys:
   cat authorized_keys

5.If using the cluster-generated key:
  cat id_hpc_mpi.pub
or, if using an ECDSA key:
  cat id_ecdsa.pub

6.If the public key is not already present in authorized_keys, append it:
For the HPC key:
  cat id_hpc_mpi.pub >> authorized_keys
or for an ECDSA key:
  cat id_ecdsa.pub >> authorized_keys

Important: Always use >> and not >. The >> operator appends the public key to the existing authorized_keys file, whereas > overwrites the file and may remove other authorised keys.

7.Confirm that the key has been added:
  cat authorized_keys


Information on Schrodinger modules are available via this link
[[https://www.schrodinger.com/platform/products/
]]
Currently the following Schrodinger Modules should be available:
  * AutoQSAR
  * AutoTS
  * Bioluminate
  * Canvas
  * ConfGen
  * Core Hopping
  * Desmond
  * Epik
  * Field-based QSAR
  * Glide,
  * Impact
  * Jaguar
  * Jaguar pKa
  * Knime
  * LigPrep
  * MacroModel
  * Maestro
  * MS Maestro
  * OPLS
  * P450 SOM
  * Phase
  * Piper
  * Prediction
  * Prime
  * PrimeX
  * QikProp
  * QSite
  * Shape Screening
  * SiteMap
  * XP Visualizer


When using the command line directly on Lengau cluster, in order to see all available Easy Scripts, first include/load this module - even better if your add this line to your .bashrc:

  module load chpc/easy_scripts

Then Easy Scripts such as these should be visible to you and usable via the command line:

qschrodinger_2019-4   qschrodinger_2020-3   qschrodinger_2021-1   qschrodinger_2021-4   qschrodinger_2022-4
qschrodinger_2020-1   qschrodinger_2020-4   qschrodinger_2021-2   qschrodinger_2022-1   qschrodinger_2023-2