The trajectory_binding_site_id.py Script

The script trajectory_binding_site_id.py runs SiteMap on each frame of a trajectory produced from an MxMD calculation to identify transient binding sites.

The command syntax is as follows:

$SCHRODINGER/run trajectory_binding_site_id.py <{mxmd1-out}.cms> <{mxmd2-out}.cms> <{output_basename}> -s 1 -HOST <hostname:num_cpus>

Corresponding trajectory files (.xtc) or directories (_trj) should be included in the directory of the MxMD output .cms files. Otherwise, the trajectory cannot be read. A remote host can be specified with -HOST hostname if you want to run SiteMap on a cluster. The driver job runs on the submission machine (either the local machine or the head/submission node of the cluster) to avoid transferring large MD trajectories. The -s option refers to the stride of trajectory frame extraction. You can set this number to control the total number of frames extracted and the total number of SiteMap jobs to run.

For better output structures, ensure the trajectories are aligned. You can align the trajectories with the trj_align.py script. Trajectories from the default MxMD results are already aligned.

For a description of all options, see trajectory_binding_site_id.py or run the command with the -h option.

After the job is done, an {output_basename}_out.maegz file is produced. The SiteMap sites are named as {output_basename}_site_X, and ordered by SiteScore/Dscore. The site and corresponding frame structures are grouped; the group name and receptor title indicate the frame number.