Cannot generate GAFF mol2 from Tripos mol2 file

[jchodera]

Processing the provided Tripos mol2 file for this molecule by antechamber leads to failure:

@<TRIPOS>MOLECULE
1,2,3,4,5-pentachloro-6-nitro-benzene
   14    14     1     0     0
SMALL
No Charge or Current Charge


@<TRIPOS>ATOM
      1 C1          1.8850   -1.0360   -0.1120 ca        1 MOL     -0.153400
      2 C2          2.9210   -1.6310    0.6080 ca        1 MOL      0.071500
      3 C3          2.8780   -1.6520    2.0020 ca        1 MOL      0.005700
      4 C4          1.8000   -1.0790    2.6760 ca        1 MOL      0.054600
      5 C5          0.7640   -0.4840    1.9550 ca        1 MOL      0.005700
      6 C6          0.8070   -0.4630    0.5610 ca        1 MOL      0.071500
      7 Cl1        -0.4790    0.2740   -0.3570 cl        1 MOL      0.005500
      8 Cl2        -0.5850    0.2340    2.7930 cl        1 MOL     -0.012400
      9 Cl3         1.7470   -1.1050    4.4180 cl        1 MOL     -0.009400
     10 Cl4         4.1750   -2.3960    2.8980 cl        1 MOL     -0.012400
     11 Cl5         4.2590   -2.3420   -0.2520 cl        1 MOL      0.005500
     12 N1          1.9280   -1.0150   -1.5410 no        1 MOL      0.316800
     13 O1          0.9850   -0.4760   -2.1600 o         1 MOL     -0.174500
     14 O2          2.9070   -1.5360   -2.1180 o         1 MOL     -0.174500
@<TRIPOS>BOND
     1    1    6 ar  
     2    1    2 ar  
     3    2    3 ar  
     4    3    4 ar  
     5    4    5 ar  
     6    5    6 ar  
     7    6    7 1   
     8    5    8 1   
     9    4    9 1   
    10    3   10 1   
    11    2   11 1   
    12    1   12 1   
    13   12   13 1   
    14   12   14 1   
@<TRIPOS>SUBSTRUCTURE
     1 MOL         1 TEMP              0 ****  ****    0 ROOT

To reproduce (using AmberTools 18.0):

$ antechamber -i in.mol2 -fi mol2 -o out.mol2 -fo mol2 -s 2 -at gaff2 -c bcc 

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 File --
   Status: pass
Info: Finished reading file (in.mol2).
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded   
      for those not bonded   
   Status: pass
-- Check Weird Bonds --
/Users/choderaj/miniconda/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (5) for atom (ID: 12, Name: N1).
       Please check atomic connectivity.

Even running without request for charges leads to failure

$ antechamber -i in.mol2 -fi mol2 -o out.mol2 -fo mol2

Welcome to antechamber 17.3: molecular input file processor.

acdoctor mode is on: check and diagnosis problems in the input file.
-- Check Format for mol2 File --
   Status: pass
-- Check Unusual Elements --
   Status: pass
-- Check Open Valences --
   Status: pass
-- Check Geometry --
      for those bonded   
      for those not bonded   
   Status: pass
-- Check Weird Bonds --
/Users/choderaj/miniconda/bin/to_be_dispatched/antechamber: Fatal Error!
Weird atomic valence (5) for atom (ID: 12, Name: N1).
       Please check atomic connectivity.

I could not locate the script in this repo used to generate the GAFF mol2 files, so I could not check (1) which AmberTools version, and (2) which options were used.

[davidlmobley]

@jchodera - see scripts/rebuild_freesolv.py.

For the record, since you didn't specify, this seems to be mobley_1396156.

I can process this molecule correctly on my laptop where I am running ambertools from AMBER16.

[jchodera]

Thanks! Let me see if I can reproduce success with ambertools 16 and failure with 18!