Appendix

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

Appendix 2: SZMAP Atom Properties

szmap calculations at a list of coordinates attach one or more of the following properties to the atoms that specify the coordinates coordinates. Key properties are in bold.

Complex, Apo or Ligand

Property Name (cplx, lig, or apo) Description
szmap_neut_diff_free_energy water - neutral probe free energy difference
szmap_neut_diff_enthalpy water - neutral probe enthalpy difference
szmap_neut_diff_entropy water - neutral probe entropy difference
szmap_vdw van der Waals energy
szmap_order fractional entropy loss from electrostatics
szmap_clash if point clashes, property = “CLASH”
szmap_mask clashing: 0, non-clashing: 1
szmap_vac_diff_free_energy water - vacuum probe free energy difference
szmap_vac_diff_enthalpy water - vacuum probe enthalpy difference
szmap_vac_diff_entropy water - vacuum probe entropy difference
szmap_free_energy free energy of probe water vs continuum
szmap_enthalpy enthalpy of probe water vs continuum
szmap_entropy entropy of probe water vs continuum
szmap_neutral_free_energy free energy of neutral probe vs continuum
szmap_neutral_enthalpy enthalpy of neutral probe vs continuum
szmap_neutral_entropy entropy of neutral probe vs continuum
szmap_interaction Poisson Boltzmann electrostatic interaction
szmap_psolv protein desolvation penalty
szmap_wsolv water probe desolvation penalty
szmap_intvdw interaction + van der Waals (for masking)
szmap_probe_burial fractional amount water probe is buried

(Complex - Protein - Ligand) Stabilization

Property Name (cplx - prot - lig) Description
szmap_neut_diff_stbl_free_energy neutral free energy difference stabilization
szmap_neut_diff_stbl_enthalpy neutral enthalpy difference stabilization
szmap_neut_diff_stbl_entropy neutral entropy difference stabilization
szmap_stbl_vdw van der Waals energy stabilization
szmap_stbl_order fractional entropy loss (ES) stabilization
szmap_stbl_clash if point clashes, property = “CLASH”
szmap_stbl_mask clashing: 0, non-clashing: 1
szmap_vac_diff_stbl_free_energy vacuum free energy difference stabilization
szmap_vac_diff_stbl_enthalpy vacuum enthalpy difference stabilization
szmap_vac_diff_stbl_entropy vacuum entropy difference stabilization
szmap_stbl_free_energy probe water free energy stabilization
szmap_stbl_enthalpy probe water enthalpy stabilization
szmap_stbl_entropy probe water entropy stabilization
szmap_stbl_neutral_free_energy neutral probe free energy stabilization
szmap_stbl_neutral_enthalpy neutral probe enthalpy stabilization
szmap_stbl_neutral_entropy neutral probe enthalpy stabilization
szmap_stbl_interaction Poisson Boltzmann electrostatic interaction
szmap_stbl_psolv protein desolvation stabilization
szmap_stbl_wsolv water probe desolvation stabilization
szmap_stbl_intvdw interaction + van der Waals stabilization
szmap_stbl_probe_burial fractional probe burial stabilization