You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Describe the bug
I ran APBS using a PDB file for a protein complex. But APBS was aborted and got the following error message. How to fix this issue?
log file
This executable compiled on May 30 2019 at 19:36:46
Parsing input file Myo1_Myo1.in...
rank 0 size 1...
read
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from Myo1_Myo1.pqr.
63126 atoms
Centered at (5.216e+01, 5.426e+01, -7.410e+00)
Net charge -4.00e+01 e
Preparing to run 2 PBE calculations.
CALCULATION #1: MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 93259.980 MB total, 93259.980 MB high water
Using cubic spline charge discretization.
Grid dimensions: 545 x 801 x 929
Grid spacings: 0.777 x 0.807 x 0.811
Grid lengths: 422.617 x 645.682 x 752.906
Grid center: (52.160, 54.262, -7.410)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Vbuildband: dpbfa problem: 1
Vbuildband: leading principle minor not PD...
Vbuildops: Changing your mgsolv to iterative
Total electrostatic energy = -NAN kJ/mol
Calculating forces...
CALCULATION #2: MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
munmap_chunk(): invalid pointer
Aborted (core dumped)
Hi APBS developers,
Describe the bug
I ran APBS using a PDB file for a protein complex. But APBS was aborted and got the following error message. How to fix this issue?
log file
This executable compiled on May 30 2019 at 19:36:46
Parsing input file Myo1_Myo1.in...
rank 0 size 1...
read
Parsed input file.
Got paths for 1 molecules
Reading PQR-format atom data from Myo1_Myo1.pqr.
63126 atoms
Centered at (5.216e+01, 5.426e+01, -7.410e+00)
Net charge -4.00e+01 e
Preparing to run 2 PBE calculations.
CALCULATION #1: MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
Debye length: 0 A
Current memory usage: 93259.980 MB total, 93259.980 MB high water
Using cubic spline charge discretization.
Grid dimensions: 545 x 801 x 929
Grid spacings: 0.777 x 0.807 x 0.811
Grid lengths: 422.617 x 645.682 x 752.906
Grid center: (52.160, 54.262, -7.410)
Multigrid levels: 4
Molecule ID: 1
Linearized traditional PBE
Single Debye-Huckel sphere boundary conditions
0 ion species (0.000 M ionic strength):
Solute dielectric: 2.000
Solvent dielectric: 78.540
Using "molecular" surface definition;harmonic average smoothing
Solvent probe radius: 1.400 A
Temperature: 298.150 K
Electrostatic energies will be calculated
Vbuildband: dpbfa problem: 1
Vbuildband: leading principle minor not PD...
Vbuildops: Changing your mgsolv to iterative
Total electrostatic energy = -NAN kJ/mol
Calculating forces...
CALCULATION #2: MULTIGRID
Setting up problem...
Vpbe_ctor: Using max ion radius (0 A) for exclusion function
munmap_chunk(): invalid pointer
Aborted (core dumped)
To Reproduce
Steps to reproduce the behavior:
Server: CentOS
Thank you so much for your help!
Best,
Yuntao Yang
The text was updated successfully, but these errors were encountered: