Running GLIDE
on Minerva
Screening with Glide involves the following steps:
- Create the target file in Maestro (.mae) format
- Create/obtain the ligand library in .mae format
- Generate the grid
- Run the screening
While all these steps can be achieved using the Maestro GUI, running
the screening on Minerva requires that Maestro be run on Minerva too
(across the network). The procedure described here performs these tasks
in the command line mode.
The above four tasks can be performed with the script
fullscreen.csh.
The script will execute the following steps:
- Ask for the macromolecule name MACRO.ext where ext can be
mae, sdf or mol2
- Create a directory MACRO_dock_G where the files will be created
(unless it is already present - in that case it offers to delete it first)
- If the extension of MACRO is not mae it will run Schrodinger's
Prepwizard
- Ask for the name of the ligand library file
- If the library is not in .mae format, it will either run Schrodinger's
Ligprep interactively (reasonable for a library of a few hundred molecules)
or print the instructions to be copied into a script running in an LSF queue.
- It will ask if induced fit runs are requested
- For runs not using induced fit the grid files will be created
(unless they are present); the user has to specify
the grid center coordinates and extensions.
- Either submit the screening job or print instructions how to do it.
- Induced fit runs require the template file IF_glide_template.in.
Experienced users can edit the template file to change the various parameters
of the runs.
- Either type of run requires an apropriate entry in the users
~/.schrodinger/schrodinger.hosts file.
The script will provide a list of the entries found; if neither is apropriate
or the file is missing the script will provide an apropriate entry.
Care must be taken that all steps are performed with the same version of
Schrodinger software.
It is also possible to run all preparatory steps on a local workstation
and use Minerva only for the Glide runs. In that case the user has to
create the directory MACRO_dock_G and copy all files created
by the Maestro there (including the target .mae file and the ligand library;
the latter can be represented by a link).
The target .mae file also has to be present where the directory
MACRO_dock_G is.
The files fullscreen.csh and IF_glide_template.in can be copied
from /sc/hydra/projects/mezeim01b/fullscreen.
Last modified: 06/13/2020