Exercise Two: Use PDB file

In this exercise, we will see how to use .pdb files in NextGenPB.

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Step 1 – Prepare the Inputs

Go to the directory for the second exercise:

cd ~/ngpb_tutorial/ex2

This will be your working directory:

~/ngpb_tutorial/ex2

Copy a .pdb file into your current directory:

cp ../NextGenPB/data/1CCM.pdb .

.pdb files do not contain partial charges or atomic radii, which are necessary to compute the molecular surface and electrostatics. These data are included in .pqr files.

So you must also copy the files that provide this information:

cp ../NextGenPB/data/charge.crg .
cp ../NextGenPB/data/radius.siz .

Understand the Required Input Files

.pdb files contain atom names, coordinates, and connectivity, but they do not include atomic charges or van der Waals radii, which are required to compute electrostatic interactions and molecular surfaces.

To provide this missing information, NextGenPB uses two additional files:

charge.crg – Partial Charges

This file assigns partial charges to atoms based on their names and residue types. Each line typically follows the format:

! This file was created from amber98.prm
!    file from TINKER package
! The format of this file:
! Column 1-6: atom name; column 7-9: residue name;
! column 10-12: residue number; column 14: chain name;
! column 15-23: charge magnitude. For example:
atom__resnumbc_charge_
1H              0.0906 !!! Hydrogen of CA backbone
2H              0.0906
3H              0.0906

H1              0.4240 !!! Hydrogen for N-terminal residue
H2              0.4240 !!!
H3              0.4240 !!!

N     ALA      -0.4157
H     ALA       0.2719
CA    ALA       0.0337
HA    ALA       0.0823
CB    ALA      -0.1825
...

radius.siz – Atomic Radii

This file assigns atomic radii used to define the molecular surface and mesh discretization. The format is similar to charge.crg:

! This file was created from amber98.prm
!    file from TINKER package
! The format of this file:
! Column 1-6: atom name; column 7-9: residue name;
! column 10-12: residue number; column 14: chain name;
! column 15-23: atom size. For example:
atom__resnumbc_radius_
1H              1.250
2H              1.250
3H              1.250
H1              1.250
H2              1.250
H3              1.250

OXT             1.480

N     ALA       1.8240
H     ALA       0.6000
CA    ALA       1.9080
HA    ALA       1.3870
CB    ALA       1.9080
...

If you already have a .pqr file (which includes charges and radii), you don’t need .crg and .siz files. However, using .pdb + .crg + .siz gives more flexibility and allows you to apply consistent parameter sets to multiple structures.

Prepare the Parameter File

Create a file named options.prm in the current directory with the following content:

[input]
filetype = pdb
filename = 1CCM.pdb
radius_file = radius.siz
charge_file = charge.crg
write_pqr = 1
name_pqr = 1CCM_out.pqr
[../]

[mesh]
mesh_shape = 0
perfil1 = 0.95
perfil2 = 0.2
scale   = 2.0
[../]

[model]
bc_type = 1                                
molecular_dielectric_constant = 2      # Dielectric constant inside the molecule
solvent_dielectric_constant   = 80     # Dielectric constant of the solvent (e.g., water)
ionic_strength                = 0.145  # Ionic strength (mol/L)
T                             = 298.15 # Temperature in Kelvin
calc_energy    = 2
calc_coulombic = 1
[../]

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Step 2 – Run the Solver

Now launch the simulation using Apptainer:

apptainer exec --pwd /App --bind .:/App ../NextGenPB.sif mpirun -np 4 ngpb --prmfile options.prm

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Step 3 – Output and Results

At the end of the execution, you will see a log similar to this:

================ [ Electrostatic Energy ] =================
  Net charge [e]:                                 1.000100072473288
  Flux charge [e]:                                0.9999852578120542
  Polarization energy [kT]:                       -370.6199322776101
  Direct ionic energy [kT]:                       -0.3187630925742346
  Coulombic energy [kT]:                          -10069.09853443279
  Sum of electrostatic energy contributions [kT]: -10440.03722980297
===========================================================
compute energy
Elapsed time : 140.616ms

Timing Report:
...

You should also see a new file called 1CCM_out.pqr.

This is the .pqr file automatically generated by NextGenPB from the .pdb input.

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➡️ Go to the next exercise.