Appendix 1: SZMAP Grids

Here is a list of all the grids that can be produced by SZMAP. By default, only a subset of these are written to the results file. The default output grids are in bold. Bump means the point failed a quick bump-check and clash means the intvdw > cutoff.

Protein + Ligand Complex

Grid Name (prot + lig complex) Description
neut_diff_free_energy_grid water - neutral probe free energy difference
neut_diff_enthalpy_grid water - neutral probe enthalpy difference
neut_diff_entropy_grid water - neutral probe entropy difference
vdw_grid van der Waals energy
order_grid fractional entropy loss from electrostatics
mask_grid clash: 0, bulk solvent: 0.98, no clash: 1.01
point_grid bump: 0, bulk solvent: 0.98, calc: 1.01
vac_diff_free_energy_grid water - vacuum probe free energy difference
vac_diff_enthalpy_grid water - vacuum probe enthalpy difference
free_energy_grid free energy of probe water vs continuum
enthalpy_grid enthalpy of probe water vs continuum
entropy_grid entropy of probe water vs continuum
neutral_free_energy_grid free energy of neutral probe vs continuum
neutral_enthalpy_grid enthalpy of neutral probe vs continuum
neutral_entropy_grid entropy of neutral probe vs continuum
interaction_grid Poisson Boltzmann electrostatic interaction
psolv_grid protein desolvation penalty
wsolv_grid water probe desolvation penalty
intvdw_grid interaction + van der Waals (for masking)
probe_burial_grid fractional amount water probe is buried

Ligand Only

Grid Name (ligand only) Description
neut_diff_lig_free_energy_grid water - neutral probe free energy difference
neut_diff_lig_enthalpy_grid water - neutral probe enthalpy difference
neut_diff_lig_entropy_grid water - neutral probe entropy difference
lig_vdw_grid van der Waals energy
lig_order_grid fractional entropy loss from electrostatics
lig_mask_grid clash: 0, bulk solvent: 0.98, no clash: 1.01
lig_point_grid bump: 0, bulk solvent: 0.98, calc: 1.01
vac_diff_lig_free_energy_grid water - vacuum probe free energy difference
vac_diff_lig_enthalpy_grid water - vacuum probe enthalpy difference
lig_free_energy_grid free energy of probe water vs continuum
lig_enthalpy_grid enthalpy of probe water vs continuum
lig_entropy_grid entropy of probe water vs continuum
neutral_lig_free_energy_grid free energy of neutral probe vs continuum
neutral_lig_enthalpy_grid enthalpy of neutral probe vs continuum
neutral_lig_entropy_grid entropy of neutral probe vs continuum
lig_interaction_grid Poisson Boltzmann electrostatic interaction
lig_psolv_grid protein desolvation penalty
lig_wsolv_grid probe desolvation penalty
lig_intvdw_grid interaction + van der Waals (for masking)
lig_probe_burial_grid fractional amount water probe is buried

Protein Only

Grid Name (protein only) Description
neut_diff_apo_free_energy_grid water - neutral probe free energy difference
neut_diff_apo_enthalpy_grid water - neutral probe enthalpy difference
neut_diff_apo_entropy_grid water - neutral probe entropy difference
apo_vdw_grid van der Waals energy
apo_order_grid fractional entropy loss from electrostatics
apo_mask_grid clash: 0, bulk solvent: 0.98, no clash: 1.01
apo_point_grid bump: 0, bulk solvent: 0.98, calc: 1.01
vac_diff_apo_free_energy_grid water - vacuum probe free energy difference
vac_diff_apo_enthalpy_grid water - vacuum probe enthalpy difference
apo_free_energy_grid free energy of probe water vs continuum
apo_enthalpy_grid enthalpy of probe water vs continuum
apo_entropy_grid entropy of probe water vs continuum
neutral_apo_free_energy_grid free energy of neutral probe vs continuum
neutral_apo_enthalpy_grid enthalpy of neutral probe vs continuum
neutral_apo_entropy_grid entropy of neutral probe vs continuum
apo_interaction_grid Poisson Boltzmann electrostatic interaction
apo_psolv_grid protein desolvation penalty
apo_wsolv_grid probe desolvation penalty
apo_vdw_grid van der Waals energy
apo_intvdw_grid interaction + van der Waals (for masking)
apo_probe_burial_grid fractional amount water probe is buried

(Complex - Protein - Ligand) Stabilization

Grid Name (cplx - prot - lig) Description
neut_diff_stbl_free_energy_grid neutral free energy difference stabilization
neut_diff_stbl_enthalpy_grid neutral enthalpy difference stabilization
neut_diff_stbl_entropy_grid neutral entropy difference stabilization
stbl_vdw_grid van der Waals stabilization
stbl_order_grid fractional entropy loss (ES) stabilization
stbl_mask_grid clash: 0, bulk solvent: 0.98, no clash: 1.01
vac_diff_stbl_free_energy_grid vacuum free energy difference stabilization
vac_diff_stbl_enthalpy_grid vacuum enthalpy difference stabilization
stbl_free_energy_grid probe water free energy stabilization
stbl_enthalpy_grid probe water enthalpy stabilization
stbl_entropy_grid probe water entropy stabilization
stbl_neutral_free_energy_grid neutral probe free energy stabilization
stbl_neutral_enthalpy_grid neutral probe enthalpy stabilization
stbl_neutral_entropy_grid neutral probe entropy stabilization
stbl_interaction_grid Electrostatic interaction stabilization
stbl_psolv_grid protein desolvation penalty stabilization
stbl_wsolv_grid water desolvation penalty stabilization
stbl_vdw_grid van der Waals stabilization
stbl_intvdw_grid interaction + van der Waals stabilization
stbl_probe_burial_grid fractional probe burial stabilization