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Gyorgy Hantal @ 4:14 pm on 05 Aug 2021

data-file generator produces error but creates LAMMPS data file

Hello,

I am glad to have found this really great tool which I was very happy to try. I uploaded some aromatic molecule to generate datafile with PCFF parameters. The code seems to run into an error (see below), but the message is not very descriptive so I have a hard time to understand what could be potentially wrong. In the end, it still generates a lammps datafile which seems to be intact.

Can you tell me please what is wrong and how should I correct the error? It seems to have a problem with identifying some atoms, but I don't know which ones. Is there a way to guide the guess somehow?

Thanks a lot!

Gyorgy

Creating bonds ...

1 molecule converted

Box size parameters read:
x: 0.000 50.000
y: 0.000 50.000
z: 0.000 50.000


Number of atoms:  49
Number of bonds:  57
Bonds have been identified
49
Getting information...
Generating PCFF atom types

Traceback (most recent call last):
  File "./data4lammps/bin/doAtomTyping.py", line 557, in 
    main(forcefield)
  File "./data4lammps/bin/doAtomTyping.py", line 545, in main
    atomlinks=AtomLink(atoms,bonds)
  File "./data4lammps/bin/doAtomTyping.py", line 60, in AtomLink
    atomlinktable[atom1-1][m1]=atom2
IndexError: list assignment index out of range
python ./data4lammps/bin/doAtomTyping.py PCFF failed w/ exit code 1

Equilibrating charge... 

Total charge= 0.0
LAMMPSDataFile.data created!

tool:struc2lammpsdf

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2 Responses

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Lorena Alzate-Vargas @ 3:28 pm on 22 Aug 2021

Could you provide the structure file you are trying to convert?

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  Gyorgy Hantal @ 6:00 pm on 27 Aug 2021
  
  I am copying a pdb file to the end of this post (don't see how I can send it otherwise). Am I supposed to specify more precisely the atom names in the pdb? I thought the type recognition is automatic based on the chemical environment.
  
  Thank you in advance!
  
  TITLE BPA
  
  REMARK THIS IS A SIMULATION BOX
  
  CRYST1 50.000 50.000 50.000 90.00 90.00 90.00 P 1 1
  
  MODEL 1
  
  ATOM 1 O BPA 1 -4.670 1.750 0.100 1.00 0.00
  
  ATOM 2 O BPA 1 4.700 1.730 -0.100 1.00 0.00
  
  ATOM 3 C BPA 1 0.000 -1.380 -0.000 1.00 0.00
  
  ATOM 4 C BPA 1 -1.290 -0.510 0.020 1.00 0.00
  
  ATOM 5 C BPA 1 1.240 -0.560 -0.020 1.00 0.00
  
  ATOM 6 C BPA 1 -0.130 -2.350 1.230 1.00 0.00
  
  ATOM 7 C BPA 1 0.020 -2.360 -1.230 1.00 0.00
  
  ATOM 8 C BPA 1 -1.440 0.330 1.070 1.00 0.00
  
  ATOM 9 C BPA 1 1.470 0.320 -1.080 1.00 0.00
  
  ATOM 10 C BPA 1 -2.160 -0.660 -0.990 1.00 0.00
  
  ATOM 11 C BPA 1 2.180 -0.680 0.990 1.00 0.00
  
  ATOM 12 C BPA 1 -2.600 1.110 1.100 1.00 0.00
  
  ATOM 13 C BPA 1 2.630 1.090 -1.100 1.00 0.00
  
  ATOM 14 C BPA 1 -3.320 0.100 -0.970 1.00 0.00
  
  ATOM 15 C BPA 1 3.340 0.090 0.960 1.00 0.00
  
  ATOM 16 C BPA 1 -3.540 0.990 0.080 1.00 0.00
  
  ATOM 17 C BPA 1 3.570 0.980 -0.080 1.00 0.00
  
  ATOM 18 H BPA 1 0.670 -3.090 1.250 1.00 0.00
  
  ATOM 19 H BPA 1 -0.120 -1.820 2.190 1.00 0.00
  
  ATOM 20 H BPA 1 -1.080 -2.910 1.180 1.00 0.00
  
  ATOM 21 H BPA 1 0.930 -2.980 -1.200 1.00 0.00
  
  ATOM 22 H BPA 1 -0.820 -3.050 -1.220 1.00 0.00
  
  ATOM 23 H BPA 1 0.040 -1.830 -2.190 1.00 0.00
  
  ATOM 24 H BPA 1 -0.720 0.430 1.870 1.00 0.00
  
  ATOM 25 H BPA 1 0.750 0.430 -1.880 1.00 0.00
  
  ATOM 26 H BPA 1 -2.050 -1.330 -1.830 1.00 0.00
  
  ATOM 27 H BPA 1 2.060 -1.350 1.830 1.00 0.00
  
  ATOM 28 H BPA 1 -2.760 1.800 1.930 1.00 0.00
  
  ATOM 29 H BPA 1 2.790 1.780 -1.930 1.00 0.00
  
  ATOM 30 H BPA 1 -4.050 0.010 -1.770 1.00 0.00
  
  ATOM 31 H BPA 1 4.070 -0.000 1.770 1.00 0.00
  
  ATOM 32 H BPA 1 -4.650 2.310 0.900 1.00 0.00
  
  ATOM 33 H BPA 1 4.690 2.290 -0.900 1.00 0.00
  
  TER
  
  ENDMDL
  
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Lorena Alzate-Vargas @ 9:24 pm on 02 Sep 2021

Hi,

I looked at the PBD file you copy here and I could not reproduce any error. The number of atoms were 33 and it successfully converted it without errors. Also, check that your file is in the correct format, I noticed some errors with the file that could be problematic, more information in this link.

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  Gyorgy Hantal @ 1:11 pm on 06 Sep 2021
  
  Hi,
  
  Thank you for checking! This is very weird, then perhaps it's me who does something silly...
  
  I just tried to convert the above file (the last two weeks I was on holiday, so didn't get to try it again before), by letting struct2lammps get the box data from the pdb, and setting the bond scale to 1.6. However, the program fails now giving a( not very insightful) error. Perhaps we are not using the same additional input. Could you please make the output generated available by sending to me at gyorgy.hantal at gmail.com (or uploading where it's convenient)?
  
  Thank you again for your help with trouble shooting!
  
  Gyorgy
  
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