Table 1.
Important input and output files generated by Ligand Binder and during the FEP/MD simulations.
| Filename | Description | ||
|---|---|---|---|
| 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 | ||