There are concatenated fields in PQR output

[wt12318]

Hi,

I have used the pdb2pqr30 with APBS:

pdb_delhetatm test_6EJG_D_1.pdb > /home/wt/tmp/test_6EJG_D_1.pdb
pdb2pqr30 --ff=PARSE /home/wt/tmp/test_6EJG_D_1.pdb /home/wt/tmp/test_6EJG_D_1.pqr
apbs --output-file=/home/wt/car_tmp/test_6EJG_D_1_out --output-format=flat /home/wt/tmp/test_6EJG_D_1_apbs_in_manual

The test_6EJG_D_1_apbs_in_manual is :

# READ IN MOLECULES
read
  mol pqr /home/wt/tmp/test_6EJG_D_1.pqr
end
elec name solv # Electrostatics calculation on the solvated state
  mg-manual # Specify the mode for APBS to run
  dime 97 97 97 # The grid dimensions
  nlev 4 # Multigrid level parameter
  grid 1 1 1 # Grid spacing
  gcent mol 1 # Center the grid on molecule 1
  mol 1 # Perform the calculation on molecule 1
  lpbe # Solve the linearized Poisson-Boltzmann equation
  bcfl sdh # Use all multipole moments when calculating the potential
  pdie 2.0 # Solute dielectric
  sdie 78.54 # Solvent dielectric
  chgm spl2 # Spline-based discretization of the delta functions
  srfm mol # Molecular surface definition
  srad 1.4 # Solvent probe radius (for molecular surface)
  swin 0.3 # Solvent surface spline window (not used here)
  sdens 10.0 # Sphere density for accessibility object
  temp 298.15 # Temperature
  calcenergy comps # Calculate energies
  calcforce no # Do not calculate forces
  write pot dx /home/wt/tmp/test_6EJG_D_1.pqr
end
quit

But some error happened:

Reading PQR-format atom data from /home/wt/car_tmp/test_6EJG_D_1.pqr.
Valist_readPQR:  Error parsing atom 1!
Please double check this atom in the pqr file, e.g., make sure there are no concatenated fields.
Error reading molecules!

When I check the PQR file, I found that there is no separator between the sixth and seventh columns:

head /home/wt/tmp/test_6EJG_D_1.pqr
ATOM      1  N   ILE     2      33.717-119.064  23.053 -0.3200 2.0000
ATOM      2  CA  ILE     2      32.405-119.605  23.528  0.3300 2.0000
ATOM      3  C   ILE     2      32.402-121.089  23.232  0.5500 1.7000
ATOM      4  O   ILE     2      32.889-121.500  22.186 -0.5500 1.4000
ATOM      5  CB  ILE     2      31.257-118.874  22.817  0.0000 2.0000
ATOM      6  CG1 ILE     2      31.315-117.340  23.047  0.0000 2.0000
ATOM      7  CG2 ILE     2      29.890-119.438  23.266  0.0000 2.0000
ATOM      8  CD1 ILE     2      30.279-116.557  22.230  0.0000 2.0000
ATOM      9  H   ILE     2      33.761-118.091  23.261  0.3300 0.0000
ATOM     10  HA  ILE     2      32.419-119.498  24.511  0.0000 0.0000

The file I use in here: test_6EJG_D_1.zip.
How to fix this problem?

Thanks.

[sobolevnrm]

Hello --

The PDB2PQR --whitespace option should fix this problem for you. You can get more information about the option by running pdb2pqr30 --help.

Thank you,

Nathan

[wt12318]

Thanks for reply. I solved this problem by add -whitespace option, but why not add this option as default?