FEP+ Input and Output Files and Directories
The input files and directories are listed below:
jobname_pv.maegz
|
input pose-viewer file containing the structures of the protein and all the ligands. |
jobname.fmp
|
input fmp file containing information on how the ligands are connected into a graph, where each edge of the graph represents a perturbation. |
jobname.sh
|
shell script to run the FEP mapper job. |
restart_jobname.sh
|
shell script to restart the FEP mapper job if the calculations for some edges fail. |
extend_jobname.sh
|
shell script to extend the calculation for certain edges of the FEP mapper jobs for another 5ns after the initial 5 ns finish.This script adds time to the final state calculation only. |
$FF_DIR
|
subdirectory (folder) containing the custom force-field parameters specified in the Preferences Panel, under Jobs − Force field. |
The output files are listed below.:
jobname.fmp
|
contains predicted affinities, graph, simulation details, and structures |
jobname.fmpdb
|
contains representative structures and trajectories for edges and for solvent and complex legs. |