I have been trying to run APBS on pymol but it always get terminated abruptly with the following error:
In show error 1
Segmentation fault (core dumped)
When select "set grid", the following popups
GENERATING PQR FILE via PDB2PQR
Erasing contents of /home/srinivasanh/pymol/pymol-generated.pdb in order to generate new PDB file
Erasing contents of /home/srinivasanh/pymol/pymol-generated.pdb in order to clean it up
TESTING
DONE TESTING
args are now converted to string: /usr/local/packages/pdb2pqr-src-2.1.0/pdb2pqr.py --ff=AMBER /home/srinivasanh/pymol/pymol-generated.pdb /home/srinivasanh/pymol/pymol-generated.pqr
PDB2PQR - a Python-based structural conversion utility
Please cite your use of PDB2PQR as:
Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA.
PDB2PQR: an automated pipeline for the setup, execution,
and analysis of Poisson-Boltzmann electrostatics calculations.
Nucleic Acids Research 32 W665-W667 (2004).
Traceback (most recent call last):
File "/usr/local/packages/pdb2pqr-src-2.1.0/pdb2pqr.py", line 62, in <module>
mainCommand(sys.argv)
File "/usr/local/packages/pdb2pqr-src-2.1.0/main.py", line 740, in mainCommand
include_old_header = options.include_header)
File "/usr/local/packages/pdb2pqr-src-2.1.0/main.py", line 281, in runPDB2PQR
myProtein = Protein(pdblist, myDefinition)
File "/usr/local/packages/pdb2pqr-src-2.1.0/src/protein.py", line 121, in init
myResidue = self.createResidue(residue, previousAtom.resName)
AttributeError: 'NoneType' object has no attribute 'resName'
PDB2PQR's mainCommand returned 1
In show error 2
Segmentation fault (core dumped)
I have compiled pymol 1.8.2 manually then added Pymol-script-repo through pymolwiki guide which installs APBS 1.4.1 and APBS Tools 2.1. ABPS pymolwiki guide
Running system
Distributor ID: Ubuntu
Description: Ubuntu 14.04.4 LTS
Release: 14.04
Codename: trusty
And the following dependencies are installed
sudo apt-get install python python-dev python-pmw python-numpy freeglut3-dev libglew-dev libpng12-dev libfreetype6-dev build-essential libxml++2.6-dev build-essential
GPU Drivers
+------------------------------------------------------+
| NVIDIA-SMI 4.304... Driver Version: 304.131 |
|-------------------------------+----------------------+----------------------+
| GPU Name | Bus-Id Disp. | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util Compute M. |
|===============================+======================+======================|
| 0 GeForce GTS 250 | 0000:03:00.0 N/A | N/A |
| 4% 47C N/A N/A / N/A | 39% 402MB / 1023MB | N/A Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Compute processes: GPU Memory |
| GPU PID Process name Usage |
|=============================================================================|
| 0 Not Supported |
+-----------------------------------------------------------------------------+
I have been looking around for alternatives, have also tried ubuntu repository installation of pymol 1.7.0.0.
Can anyone give me some advise? Thank you~
