Issue of improper dihedral angles: atom indices are shuffled

[kobaya-sh]

• [x] I believe this to be a bug with LigParGen
• [ ] This is a feature request

Issue Information

Software name & Version : (this issue can be found only from the output of LigParGen server) Method:

I found the problem that the improper dihedral angles are printed in strange order when I submitted the molecules including phenyl group.

For the simplest case, the problem occurs in the case of benzene (the attachment).

I checked this problem occurs in the following formats (if I correctly understand the file formats):

• .lmp
• .key
• .top
• .xml

  Expected Behavior

In the case of .rtf, which seems correct (sorry, I am not familiar with this format), the corresponding output is shown as follows:

{ Improper Dihedrals: aType1 aType2 aType3 aType4 kt period phase }
IMPRoper H806   C800   C801   C805 2.50000 2 180.00000 
IMPRoper H807   C801   C800   C802 2.50000 2 180.00000 
IMPRoper H808   C802   C801   C803 2.50000 2 180.00000 
IMPRoper H809   C803   C802   C804 2.50000 2 180.00000 
IMPRoper H810   C804   C803   C805 2.50000 2 180.00000 
IMPRoper H811   C805   C800   C804 2.50000 2 180.00000 
IMPRoper    X      X      X      X  0.000     1     0.00  ! WILD CARD FOR MISSING IMPROPER 

In this case, the center of the dihedral angles (maybe the third column, C800, C801, ...) seems always the carbon atoms. I infer from .rtf that the corresponding part in .lmp file is expected to be as follows:

Impropers

     1      1      7      1      2      6
     2      2      8      2      1      3
     3      3      9      3      2      4 
     4      4     10      4      3      5 
     5      5     11      5      4      6 
     6      6     12      6      1      5 

Actual Behavior

On the other hand, the corresponding output in the actual .lmp file is as follows.

Impropers

     1      1      1      2      6      7 
     2      2      2      1      3      8 
     3      3      3      9      2      4 
     4      4      4     10      3      5 
     5      5      5     11      4      6 
     6      6      6      1     12      5 

The fourth column (2, 1, 9, ...) shows the center of the improper dihedral angles. The atoms 9-11 are hydrogen, which should not be the center, because the center is bonding to at least three atoms.

Thank you in advance.

UNK_6D7018.zip