Error in 'solvation free energy' (box setting error)

[ru80john]

Hello!

I'm a new user of Poltype2, and I successfully generate 'final.xyz' and 'final.key' files for my molecule. However, I encountered a problem in that I could not run the solvation free energy calculation. It ended in the very beginning. The error is shown below:

Fri Nov 29 17:33:53 2024 Computing volume

Traceback (most recent call last):
  File "/home/ru80john/package/master/PoltypeModules/poltype.py", line 8254, in <module>
    RunPoltype()
  File "/home/ru80john/package/master/PoltypeModules/poltype.py", line 8227, in RunPoltype
    poltype=PolarizableTyper()
  File "<string>", line 417, in __init__
  File "/home/ru80john/package/master/PoltypeModules/poltype.py", line 1379, in __post_init__
    self.MolecularDynamics()
  File "/home/ru80john/package/master/PoltypeModules/poltype.py", line 2282, in MolecularDynamics
    ann.main(self)
  File "/home/ru80john/package/master/PoltypeModules/annihilation.py", line 37, in main
    box.BoxSetupProtocol(poltype)
  File "/home/ru80john/package/master/PoltypeModules/boxsetup.py", line 793, in BoxSetupProtocol
    maxdirection,numberofsubboxes,subaaxislist,subbaxislist,subcaxislist,subvolumelist=ComputeBoxSize(poltype)
  File "/home/ru80john/package/master/PoltypeModules/boxsetup.py", line 43, in ComputeBoxSize
    longestdim=FindDimensionsOfMoleculeTinker(poltype,poltype.outputpath+xyz)
  File "/home/ru80john/package/master/PoltypeModules/boxsetup.py", line 264, in FindDimensionsOfMoleculeTinker
    vec=np.array([float(linesplit[2]),float(linesplit[3]),float(linesplit[4])])
IndexError: list index out of range

It seems like the procedure in the box setting is not successful.

Are there other possibilities that could cause this problem? Or maybe I gave the wrong setting.
I list the 'final.xyz', 'final.key' and 'poltype.ini' below.

Any help would be greatly appreciated.

Thank you very much!

poltype.ini

ligandxyzfilenamelist=final.xyz
keyfilenamelist=final.key

final.xyz

    20 xxx
     1  C     -1.463187   -1.171217   -0.098045      401    2     5     7
     2  O     -0.217909   -1.206945   -0.634979      402    1     3
     3  C      0.259241    0.133833   -0.817236      403    2     4     6    12
     4  C     -0.898447    1.004011   -0.418683      404    3     5    10
     5  C     -1.887897    0.224688    0.023994      405    1     4     8
     6  H      0.519207    0.250440   -1.875672      413    3
     7  O     -2.104214   -2.146417    0.205432      406    1
     8  O     -3.090295    0.557369    0.536761      407    5     9
     9  H     -3.521996   -0.277703    0.779262      414    8
    10  O     -0.763896    2.340724   -0.476583     408    4    11
    11  H     -1.354371    2.740427    0.176178     415   10
    12  C      1.505069    0.370576    0.026028     409    3    13    14    16
    13  H      1.898822    1.357668   -0.262175     416   12
    14  O      1.154660    0.349839    1.390281     410   12    15
    15  H      1.887673    0.751096    1.871624     417   14
    16  C      2.605936   -0.637902   -0.276560     411   12    17    18    19
    17  H      2.651062   -0.845970   -1.357035     418   16
    18  H      2.376066   -1.573163    0.247702     418   16
    19  O      3.813020   -0.046456    0.174141     412   16    20
    20  H      4.488313   -0.731630    0.222704     419   19

final.key
final.txt