How to use Blastermaster 2.0 on UCSF computers

Using Blastermaster 2.0

0. Copy the relevant input files to your directory

Copy your rec.pdb and xtal-lig.pdb files to your directory. If you want to provide your own rec.crg.pdb, copy that in too. Blastermaster 2.0 will look for these in the directory in which you run it (or at whichever file paths you set for their corresponding parameters in the config file).

1. Source the relevant pre-configured environment

Gimel

source /nfs/soft2/ian/env.sh

If you are using Gimel, be aware that you will need to ssh to a node that supports Python >=3.8.5. E.g.:

ssh n-9-38

By default, the pre-configured environment uses DOCK-3.8.0. If you want to use a different version of DOCK, set the DOCKBASE parameter to the path of the desired DOCK repository:

export DOCKBASE=<ABSOLUTE_PATH_TO_DOCK_REPOSITORY>

2. Generate a blaster config file to your directory

The following will generate a file called "blasterconfig.yaml"

blasterconfig

The following will generate a file called whatever you put for <BLASTER_CONFIG_FILE_NAME>

blasterconfig <BLASTER_CONFIG_FILE_NAME>

3. Edit the blaster config file to your specifications

The parameters in the config file govern the behavior of blastermaster.

Note: if you are using your own files other than rec.pdb and xtal-lig.pdb (e.g., rec.crg.pdb), you need to point to them in the "existing_files_to_use_section". E.g., receptor_charged_file should be set to "rec.crg.pdb" if you have copied it into the directory you are working in.

To enter the vi text editor:

vi <BLASTER_CONFIG_FILE_NAME>

To enter edit-mode, press "i".

Make your edits.

When you're done, press "ESC" to exit edit-mode.

Press "x!" followed by "RETURN" to save your edits and exit the text editor.

4. Run

blastermaster <BLASTER_CONFIG_FILE_NAME>

Tips for users

You can create and save multiple blaster config files with different settings so long as they have different names (e.g. blasterconfig_default.yaml, blasterconfig_use_existing_charged_receptor.yaml). Then it is easy to reuse the same configuration settings at a later time.