Setting variable protein_alone to the default value n
Setting variable name_xtc to the default value npt
Setting variable name_tpr to the default value npt

 WARNING!! Multiple files are assigned to the itp_receptor variable. It is ok if there are more files describing the topology of the protein 


You are using the option "use_topology".

Setting variable multichain to the default value n
Setting variable read_vdw_radii to the default value n
Setting variable extraspace to the default value 5
Setting variable coarsefactor to the default value 1.7
Setting variable grid_spacing to the default value 0.5
Setting variable sdie to the default value 80
Setting variable chgm to the default value spl2
Setting variable srfm to the default value smol
Setting variable srad to the default value 1.4
Setting variable swin to the default value 0.3
Setting variable sdens to the default value 10.0
Setting variable calcforce to the default value no
Setting variable ion_ch_pos to the default value 1
Setting variable ion_rad_pos to the default value 2.000
Setting variable ion_conc_pos to the default value 0.1500
Setting variable ion_ch_neg to the default value -1
Setting variable ion_rad_neg to the default value 2.000
Setting variable ion_conc_neg to the default value 0.1500
Setting variable Hsrfm to the default value sacc
Setting variable Hpress to the default value 0.000
Setting variable Hgamma to the default value 0.0227
Setting variable Hdpos to the default value 0.20
Setting variable Hcalcforce to the default value total
Setting variable Hxgrid to the default value 0.1
Setting variable Hygrid to the default value 0.1
Setting variable Hzgrid to the default value 0.1
 
################################################################ 
Here you'll find the recap of the processes 
################################################################ 
 
The binding free energy (DG_bind) will be calculated by the 
MM/MPBSA method as (eqn.1)
       DG_bind = < G_complex - G_protein - G_ligand >        (1) 
where the G_complex, G_protein and G_ligand are the free 
energies of complex, protein and ligand respectively. The 
brackets indicate that the average of snapshots taken from a 
single MD trajectory will be considered. 
The free energy of each state is calculated as (eqn.2): 
              G = E_MM + G_PB + G_SA - TS                    (2) 
TS is the entropic contribution of the solute, which will not be
evaluated in the first version of this script. 
G_PB and G_SA are the contributions from polar and nonpolar 
terms of the free energy of the solvent continuum, the first 
being calculated via the Poisson-Bolztmann equation and the 
latter being calculated as (eqn.3)
                  G_SA = g SASA + b                          (3) 
where g is the surface tension proportionality constant, b is 
the free energy of nonpolar solvation for a point solute and 
SASA is the solvent accessible surface area. 
E_MM is the molecular mechanical energy, calculated as the sum 
of different contributions (eqn.4) 
              E_MM = E_vdW + E_ele + E_int                   (4) 
E_vdW, E_ele are the van der Waals (LJ) and the electrostatic 
energies, respectively. 
E_int is the internal energy including bond, angle and torsional 
angle energies. It is worth noting that in the case of 
single-trajectory experiments, the variation of E_int (DE_int)
equals zero in calculating the binding free energy according to 
eqn.1, since the internal energies of the complex and the 
separated parts (protein and ligand) are calculated from the 
same trajectory. 
 
These terms will be calculated and stored in REP files (one for 
each PDB file) separatedly. 
 
 
 

======================== 
 
The complex is named System. 
The protein is named Protein. 
The ligand is named BEC. 
The operative files (xtc, tpr) are named npt and npt. 

======================== 
 
 
 
 19:21:30 
The procedure is initiated.
 
19:21:30 Generating the centered PDB structures in 1EBZ...
 

19:21:33 Started the recovery of the Coulomb/VdW energy contributions from the PDB files in 1EBZ...
20:24:44 Started generating the PQR files from the corresponding 1EBZ PDB files...
20:24:46 Started calculating the LJ parameters for 1EBZ...
20:25:05 Started calculating with the coulomb tool the Coulomb parameters for 1EBZ...
 

20:25:14 Starting parsing the PQR files' coordinates...

20:25:18 Started performing the grid mesh calculations...

20:25:18 Started generating the input files for solvation energy calculations in 1EBZ...
20:25:18 Started generating the SH files for solvation energy calculations in 1EBZ...
In the directory 1EBZ 21 PQR/PDB files have been generated to perform the APBS calculations.


20:25:19 All successfully DONE 
Run gmxpbsa1.sh to perform APBS

