# 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
Hi,
I have used the pdb2pqr30 with APBS:
The
test_6EJG_D_1_apbs_in_manual
is :But some error happened:
When I check the PQR file, I found that there is no separator between the sixth and seventh columns:
The file I use in here: test_6EJG_D_1.zip. How to fix this problem?
Thanks.