[WIP] Finish full transition to openmmforcefields (away from Topology -> OEMol)

[jchodera]

No description provided.

[jchodera]

It looks like the current failing tests are due to the mol2 files being fed into antechamber missing atom names:

(perses) lski2838:tmpgn0nav6x choderaj$ cat molecule-before-bond-perception.mol2 
@<TRIPOS>MOLECULE
naphthalene
   18    19     0     0     0
SMALL
NO_CHARGES

@<TRIPOS>ATOM
      1             0.0000    0.0000    0.0000           1 <0>         0.0000
      2             0.0000    0.0000    0.0000           1 <0>         0.0000
      3             0.0000    0.0000    0.0000           1 <0>         0.0000
      4             0.0000    0.0000    0.0000           1 <0>         0.0000
      5             0.0000    0.0000    0.0000           1 <0>         0.0000
      6             0.0000    0.0000    0.0000           1 <0>         0.0000
      7             0.0000    0.0000    0.0000           1 <0>         0.0000
      8             0.0000    0.0000    0.0000           1 <0>         0.0000
      9             0.0000    0.0000    0.0000           1 <0>         0.0000
     10             0.0000    0.0000    0.0000           1 <0>         0.0000
     11             0.0000    0.0000    0.0000           1 <0>         0.0000
     12             0.0000    0.0000    0.0000           1 <0>         0.0000
     13             0.0000    0.0000    0.0000           1 <0>         0.0000
     14             0.0000    0.0000    0.0000           1 <0>         0.0000
     15             0.0000    0.0000    0.0000           1 <0>         0.0000
     16             0.0000    0.0000    0.0000           1 <0>         0.0000
     17             0.0000    0.0000    0.0000           1 <0>         0.0000
     18             0.0000    0.0000    0.0000           1 <0>         0.0000
@<TRIPOS>BOND
     1   18   18 
     2   18   18 
     3   18   18 
     4   18   18 
     5   18   18 
     6   18   18 
     7   18   18 
     8   18   18 
     9   18   18 
    10   18   18 
    11   18   18 
    12   18   18 
    13   18   18 
    14   18   18 
    15   18   18 
    16   18   18 
    17   18   18 
    18   18   18 
    19   18   18 
(perses) lski2838:tmpgn0nav6x choderaj$ antechamber -fi mol2 -i molecule-before-bond-perception.mol2 -fo mol2 -o out.mol2

Welcome to antechamber 19.0: molecular input file processor.

acdoctor mode is on: check and diagnose problems in the input file.
-- Check Format for mol2 File --
   Status: pass

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.

Warning: Unknown bond type for bond (0.000-0.000:@<TRIPOS>BOND
).
         Assuming it is a single bond.
antechamber: Fatal Error!
Unrecognized atomic name (.0000).

The mol2 file contains

(perses) lski2838:tmpgn0nav6x choderaj$ cat molecule-before-bond-perception.mol2 
@<TRIPOS>MOLECULE
naphthalene
   18    19     0     0     0
SMALL
NO_CHARGES

@<TRIPOS>ATOM
      1             0.0000    0.0000    0.0000           1 <0>         0.0000
      2             0.0000    0.0000    0.0000           1 <0>         0.0000
      3             0.0000    0.0000    0.0000           1 <0>         0.0000
      4             0.0000    0.0000    0.0000           1 <0>         0.0000
      5             0.0000    0.0000    0.0000           1 <0>         0.0000
      6             0.0000    0.0000    0.0000           1 <0>         0.0000
      7             0.0000    0.0000    0.0000           1 <0>         0.0000
      8             0.0000    0.0000    0.0000           1 <0>         0.0000
      9             0.0000    0.0000    0.0000           1 <0>         0.0000
     10             0.0000    0.0000    0.0000           1 <0>         0.0000
     11             0.0000    0.0000    0.0000           1 <0>         0.0000
     12             0.0000    0.0000    0.0000           1 <0>         0.0000
     13             0.0000    0.0000    0.0000           1 <0>         0.0000
     14             0.0000    0.0000    0.0000           1 <0>         0.0000
     15             0.0000    0.0000    0.0000           1 <0>         0.0000
     16             0.0000    0.0000    0.0000           1 <0>         0.0000
     17             0.0000    0.0000    0.0000           1 <0>         0.0000
     18             0.0000    0.0000    0.0000           1 <0>         0.0000
@<TRIPOS>BOND
     1   18   18 
     2   18   18 
     3   18   18 
     4   18   18 
     5   18   18 
     6   18   18 
     7   18   18 
     8   18   18 
     9   18   18 
    10   18   18 
    11   18   18 
    12   18   18 
    13   18   18 
    14   18   18 
    15   18   18 
    16   18   18 
    17   18   18 
    18   18   18 
    19   18   18 

I'm not sure yet whether the failure is caused by (1) the new antechamber now requires atom names, or (2) somehow our mol2 generation is no longer adding atom names.

[hannahbrucemacdonald]

I would imagine it's a new antechamber requirement, seeing as we haven't removed adding atom names. We have this function

perses/perses/utils/openeye.py

Line 281 in a98c451

def generate_unique_atom_names(molecule):

perses.utils.gegenerate_unique_atom_names()

Do we just need to call this in the tests?

[jaimergp]

According to the changelog, antechamber hasn't received any updates since AT17. Which version were we using before? ambermini 16?

[jchodera]

This PR has been superceded by #618