Desmond Utilities

The Desmond distribution contains a number of utilities for performing a range of specific tasks, apart from those described previously. These can be run with $SCHRODINGER/run. Use the -h option to see the usage message (which is included in the documentation and linked below by the script name).

System Preparation

relax_membrane.py—relax a membrane-containing system

The relax_membrane.py script allows you to prepare a membrane relaxation through command line.

To use the membrane relaxation protocol:

1. Save your newly built protein-membrane system in a CMS file (referred to here as protein-membrane.cms).

2. Run the script to prepare the necessary input files:

   $SCHRODINGER/run relax_membrane.py -i protein-membrane.cms \
       -t temperature -j protein-membrane 

3. Run the membrane relaxation protocol using the command

   $SCHRODINGER/utilities/multisim -JOBNAME protein-membrane \
       -HOST myhost -mode umbrella -i protein-membrane-in.cms \
       -m protein-membrane.msj -o protein-membrane-out.cms \
   						-set 'stage[1].set_family.md.jlaunch_opt = ["-gpu"]'

This process may take some time since it equilibrates the system in stages for about 1.2 ns. The file protein-membrane-out.cms should be reasonably well equilibrated and can be used as input for the production simulation for your system.

rebuild_cms.py—rebuild a model system from structures

After editing the structure in a .cms file and exporting from Maestro, it will only contain the full system CT (solute and solvent are in a single entry) and lack the force field assignment. You can rebuild the full Desmond model system using this .cms file on the command line:

$SCHRODINGER/run rebuild_cms.py -make_comp_ct [-solvent_asl ASL] [-membrane_asl ASL] input.mae output.cms

The solvent and the membrane are automatically detected, but you can specify them by using ASL expressions. If the box vector is not present, the box size is estimated from the system size.

If you have a .cms file with just the component CTs instead, you can create a full model system using the following command: 

$SCHRODINGER/run rebuild_cms.py -make_full_ct input.cms output.cms

Analyzing Desmond Simulations

• analyze_simulation.py—perform geometric analyses and energy group analyses on trajectories.
• analyze_trajectory_ppi.py—analyze protein-protein interactions within trajectories.
• rdf.py—calculate the radial distribution function of selected atoms from a trajectory.
• trajectory_analyze_hbonds.py—records the number of hydrogen bonds in each frame of a trajectory.
• trajectory_asl_monitor.py—monitor the number of atom groups within a specified distance of another atom group during a trajectory.
• trajectory_bfactors.py—write a single structure with RMSF and B-factors calculated for a trajectory.
• trajectory_binding_site_id.py—run a SiteMap calculation on each frame of a trajectory to identify transient binding sites.
• trajectory_binding_site_volumes.py—run a SiteMap calculation on each frame of a trajectory.
• trajectory_dihedral.py—measure common dihedral angles for a trajectory, for example “phi”, and “psi” angles.
• trj_center.py—translate all atoms so that the specified atoms stay in the center (origin) of the simulation box.
• trj_cluster.py—cluster trajectories based on the RMSD of a specified atom selection.
• trj_essential_dynamics.py—run a protein essential dynamics analysis [36].
• trj_occupancy.py—generate a 3D occupancy map accumulated over a trajectory for a specified atom selection. The map can be imported into Maestro for display.

Manipulating Trajectories

• dtr2xtc.py—convert trajectory from DTR format to XTC format.
• frame2cms.py—convert trajectory frames to CMS files.
• trj_align.py—align a trajectory on a specified atom selection.
• trj_extract_subsystem.py—create a new CMS file and trajectory for a subsystem of the input system, defined by a specified atom selection.
• trj_info.py—print out general information about the model system and the trajectory.
• trj_merge.py—merge multiple trajectories.
• trj_parch.py—reduce the size of a trajectory by removing unneeded water molecules.
• trj_rescue.py—attempt to recover a corrupted trajectory in which some frames were not saved correctly.
• trj_slice.py—create new trajectory with a smaller number of frames.
• trj_unwrap.py—create new trajectory with the position of selected atoms unwrapped according to the model system's periodic boundary conditions.
• trj_wrap.py—create new trajectory with all atoms placed inside the simulation box.
• trj2mae.py—convert trajectory frames to plain Maestro files (.maegz).