fep_memory_estimation.py Command Help

Command: $SCHRODINGER/run -FROM scisol fep_memory_estimation.py

usage: fep_memory_estimation.py [-h]
                                (-num-atoms NUM_ATOMS | -input-structure INPUT_STRUCTURE)
                                -num-lambdas NUM_LAMBDAS
                                [-fep-type {prm_protein_binding,prm_ligand_binding,prm_thermostability,prm_stability,protein_selectivity,covalent_ligand,small_molecule,metalloprotein,ligand_selectivity,absolute_binding,solubility,lambd_prm_protein_binding,lambd_prm_ligand_binding,lambd_prm_thermostability,prm_protein_binding_ssms,prm_ligand_binding_ssms,prm_thermostability_ssms}]
                                [-solvate] [-buffer BUFFER]
                                [-water-model {SPC,SPCE,TIP3P,TIP3P_CHARMM,TIP4P,TIP4PEW,TIP4P2005,TIP5P,TIP4PD}]
                                [-box-shape {cubic,orthorhombic}]
                                [-no-counterions]

Estimate CPU and GPU memory requirements for FEP calculations

options:
  -h, --help            show this help message and exit
  -num-atoms NUM_ATOMS, -n NUM_ATOMS
                        Number of atoms in the fully solvated system (most
                        accurate if from test job)
  -input-structure INPUT_STRUCTURE, -i INPUT_STRUCTURE
                        Path to structure file (.mae, .maegz, .pdb, etc.). If
                        used without -solvate, counts atoms directly from
                        file. If used with -solvate, estimates solvated atom
                        count from unsolvated structure.
  -num-lambdas NUM_LAMBDAS, -l NUM_LAMBDAS
                        Number of lambdas (replica) that will be used in the
                        fep calculation
  -fep-type {prm_protein_binding,prm_ligand_binding,prm_thermostability,prm_stability,protein_selectivity,covalent_ligand,small_molecule,metalloprotein,ligand_selectivity,absolute_binding,solubility,lambd_prm_protein_binding,lambd_prm_ligand_binding,lambd_prm_thermostability,prm_protein_binding_ssms,prm_ligand_binding_ssms,prm_thermostability_ssms}
                        FEP type

solvation options:
  Options for estimating solvated system size (only valid with -input-
  structure)

  -solvate, -s          Estimate solvated atom count from unsolvated structure
  -buffer BUFFER        Solvation buffer width in Angstroms (default: 5.0)
  -water-model {SPC,SPCE,TIP3P,TIP3P_CHARMM,TIP4P,TIP4PEW,TIP4P2005,TIP5P,TIP4PD}
                        Water model (default: SPC)
  -box-shape {cubic,orthorhombic}
                        Solvation box shape (default: orthorhombic)
  -no-counterions       Do not add counterions for charge neutralization