STEP1 |
Input |
step1_pdbreader.inp |
To read a protein-ligand complex structure |
|
Output |
step1_pdbreader.pdb |
Structure after initialization in CHARMM |
@lig/@lig.rtf |
Ligand topology file |
@lig/@lig_g.rtf |
Ligand topology file (with atom groups) |
@lig/@lig.prm |
Ligand parameter file |
@lig/ndihe.str |
Symmetric groups found in the ligand if any |
|
STEP2 |
Input |
step2.1_site_solvator.inp |
To solvate the binding site with a water sphere (SITE) |
step2.2_bulk_solvator.inp |
To solvate the ligand with a water sphere (BULK) |
|
Output |
step2.1_site_solvator.pdb |
Solvated simulation system for SITE
|
step2.2_bulk_solvator.pdb |
Solvated simulation system for BULK
|
|
STEP3 |
Input |
step3.1_gsbp_setup.inp |
To setup GSBP simulation system for SITE
|
step3.2_ssbp_setup.inp |
To setup SSBP simulation system for BULK
|
config.py |
Contains several (user-defined) configuration variables |
step3_job.pbs |
Example PBS script for batch system |
|
Output |
step3.1_gsbp_setup.pdb |
SITE simulation system after GSBP setup |
step3.1_gsbp_setup.mij |
Calculated multipolar reaction field |
step3.1_gsbp_setup.phix |
Calculated external reaction field |
step3.2_ssbp_setup.pdb |
BULK simulation system after SSBP setup |
|
STEP4 |
Input |
step4.1_site_gcmc.inp |
To adjust the number of water molecules in GSBP |
step4.2_site_equil.inp |
To equilibrate SITE system |
step4.3_restraint_setup.inp |
To setup anchoring atoms and restraint parameters |
step4.3_restraint_geo.str |
To determine anchoring atoms |
step4.3_restraint_geotest.str |
To test validity of anchoring atoms |
step4.3_restraint_ref.str |
To determine the restraint parameters |
step4.4_bulk_equil.inp |
To equilibrate BULK system |
step4_job.pbs |
Example PBS script for batch system |
|
Output |
step4.1_site_gcmc.crd |
SITE system after adjustment of number of water |
step4.2_site_equil.dcd |
Trajectory of SITE system equilibration |
step4.2_site_equil.crd |
Last snapshot of equilibrated SITE system |
step4.3_restraint_geo.prm |
Anchoring atom definition |
step4.3_restraint_geo.pdb |
Anchoring atoms (named as DUM) |
step4.3_restraint_ref.prm |
Reference values for restraint potential |
step4.3_restraint_consdihe.str |
Symmetric group restraints |
step4.3_restraint_ligave.pdb |
Average structure of bound ligand during equilibration |
step4.4_bulk_equil.pdb |
Last snapshot of equilibrated BULK system |
|
STEP5 |
Input |
step5.1_site_fes.inp |
FEP/MD input for SITE system (including PMF input) |
step5.1_site_gconst.str |
To setup orientational/translational restraints |
step5.2_bulk_fes.inp |
FEP/MD input for BULK system (including PMF input) |
step5_jobmanager.com |
Script for submitting batch jobs |
step5_template.pbs |
Example PBS script for batch system |
|
STEP6 |
Input |
step6.1_wham_fep.inp |
WHAM input for FEP/MD simulations |
step6.1_wham_fep.pbs |
Example PBS script for batch system |
step6.2_wham_rmsd.inp |
WHAM input for PMF umbrella sampling simulations |
step6.2_wham_rmsd.pbs |
Example PBS script for batch system |
step6_wham.com |
Script for WHAM calculation |
step6_table.py |
Example script to tabulate the binding free energy |