Electrostatics/pdb2pqr

inputget error on alphafold structures

shaharsu opened this issue · 2 comments

shaharsu commented

Hi,

I have a pqr file generated from an alphafold2 pdb. I am trying to generate an input file with the following command:

python3 /opt/spack/opt/spack/linux-rhel8-icelake/gcc-11.2.0/apbs-3.4.1-xj5ly7rbs6vfdrxfabur5cgzdox6szek/share/apbs/tools/manip/inputgen.py --method=auto tmp/tmp-elec/AF2.pqr

The command exits with the following error:

Forcing a sequential calculation
Traceback (most recent call last):
  File "/opt/spack/opt/spack/linux-rhel8-icelake/gcc-11.2.0/apbs-3.4.1-xj5ly7rbs6vfdrxfabur5cgzdox6szek/share/apbs/tools/manip/inputgen.py", line 491, in <module>
    main()
  File "/opt/spack/opt/spack/linux-rhel8-icelake/gcc-11.2.0/apbs-3.4.1-xj5ly7rbs6vfdrxfabur5cgzdox6szek/share/apbs/tools/manip/inputgen.py", line 485, in main
    size.runPsize(filename)
  File "/mnt/spack/opt/spack/linux-rhel8-icelake/gcc-11.2.0/apbs-3.4.1-xj5ly7rbs6vfdrxfabur5cgzdox6szek/share/apbs/tools/manip/psize.py", line 289, in runPsize
    self.set_all()
  File "/mnt/spack/opt/spack/linux-rhel8-icelake/gcc-11.2.0/apbs-3.4.1-xj5ly7rbs6vfdrxfabur5cgzdox6szek/share/apbs/tools/manip/psize.py", line 233, in set_all
    self.setSmallest(n)
  File "/mnt/spack/opt/spack/linux-rhel8-icelake/gcc-11.2.0/apbs-3.4.1-xj5ly7rbs6vf
[AF2.zip](https://github.com/Electrostatics/pdb2pqr/files/13620394/AF2.zip)
drxfabur5cgzdox6szek/share/apbs/tools/manip/psize.py", line 174, in setSmallest
    if nsmall <= 0:
TypeError: '<=' not supported between instances of 'list' and 'int'

The same command works fine for pdb's obtained directly from the pdb website (e.g. 1UBQ). I'm attaching the initial AF2 pdb and the resulting pqr file.

shaharsu commented

Sorry - guess upload didn't work before - here it is.
AF2.zip

jbardhan commented

Ha, was JUST about to ask. Thanks! I'll have a look as soon as I can.

Thanks very much,
Jay

  • 👍1