Desmond Tutorial

Desmond Tutorial
Preparing a Desmond simulation with the System Builder
Figure 4.15 Transmembrane hole in the DPPC bilayer for 1su4
Note the large
hole within
which the
protein was
inserted.
9. More experienced users may want to run the System Builder job from the command
line. Instead of clicking the green Start button, click the Write button to write a command
script file to disk that can be executed from the command line.
a. Click the Write button in the System Builder window to write the job files to disk.
There are two input files:
— my_setup.mae. This is the Maestro structure file of the solute (1su4 protein,
calcium ions, crystal water molecules, neutralizing ions, and counterions),
which serves as the input for system setup.
— my_setup.csb. This is the command file, which can be hand‐edited for custom
setup cases. For detailed documentation of the .csb file see the Schrödinger Desmond
User Manual listed in “Documentation Resources” on page 97.
And a single output file (besides a log file):
— my_setup-out.cms. This is the Maestro structure file of the entire membrane
simulation system including OPLS‐AA force field parameters. For detailed documentation
of the .cms file see the Schrödinger Desmond User Manual listed in
“Documentation Resources” on page 97.
b. Execute the following command at the command line:
$ $SCHRODINGER/run $SCHRODINGER/utilities/system_builder
my_setup.csb
where my_setup is the file name given to “Write”.
56 D. E. Shaw Research September 2008