Structure of the complexes file
RunNb
trajectory number
StepNb
Number of the step in this trajectory
TransX
Coordinates of solute 2 center of mass: x
TransY
Coordinates of solute 2 center of mass: y
TransZ
Coordinates of solute 2 center of mass: z
Rot1X
Orientation of the solute 2: x vector coordinates along x
Rot1Y
Orientation of the solute 2: x vector coordinates along y
Rot1Z
Orientation of the solute 2: x vector coordinates along z
Rot2X
Orientation of the solute 2: y vector coordinates along x
Rot2Y
Orientation of the solute 2: y vector coordinates along y
Rot2Z
Orientation of the solute 2: y vector coordinates along z
TotEn
Total interaction energy of the complex (in kT)
El-1
electrostatic interaction energy between effective charges of the solute 1 and a electrostatic potential of the solute 2
El-2
electrostatic interaction energy between effective charges of the solute 2 and a electrostatic potential of the solute 1
ED-1
electrostatic desolvation energy of the solute 1 (or solid surface)
ED-2
electrostatic desolvation energy of the solute 2
HD-1
hydrophobic desolvation energy of solute 1 (or solid surface)
HD-1
hydrophobic desolvation energy of solute 2
LJ-1
Lennard-Jones interaction energy of the solute 2 with solute 1 (kT)
LJ-2
redundant
ImgChg-1
electrostatic image-charge energy of a solute 2 (protein) in the presence of a metal surface (solute 1, ProMetCS model)
ImgChg-2
redundant
MetDes-1
redundant
MetDes-2
Solid surface non-polar desolvation energy (ProMetCS model)
Occur
Number of equivalent complexes within the rmsd threshold (set with the parameter rmsd_min )
AvEnergy
Average energy of all equivalent complexes
StdAvEnergy
The transformation that brings the molecule from the coordinates given to the PDB file
to the coordinates in the simulation is given by:Mean square deviation of the docking complex energy for all equivalent complexes
R * (x-com) + Trans
where
com: center of mass of the molecule in the PDB file
R (Rot1, Rot2, Rot1 x Rot2) rotation matrix
For a code example, please look at auxi/generateFortComplexesPdbs-SDA7.py on how to regenerate a PDB file from the complexes file.