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

Be aware that you will need to ssh to a node that supports Python >=3.8.5 (e.g. gimel5, n-9-38). Otherwise you will run into an error like:

/lib64/libc.so.6: version `GLIBC_2.15' not found

Source a Python environment

source /nfs/soft/ian/python<PYTHON_VERSION>.sh

where <PYTHON_VERSION> is replaced with one of the available python versions. E.g.:

source /nfs/soft/ian/python3.8.5.sh

To check which python versions are available, run

ls /nfs/soft/ian/python*.sh

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.

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

If you used the default blaster config file name, then you can simply run:

blastermaster

Otherwise:

blastermaster --blaster_config_file_path=<BLASTER_CONFIG_FILE_PATH>

If you want to supply your own charged receptor file (usually called rec.crg.pdb), you can do so as follows:

blastermaster --charged_receptor_file_path=<PATH_TO_FILE>

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_elec_only_thinspheres.yaml). Then it is easy to reuse the same configuration settings at a later time.