Hi,

For quite a long time I've been trying to simulate polyphosphate ester molecules using GROMACS software with topology generated with Acpype, but with little success.

The first approach resulted in an error from Acpype:

ERROR: more than one residue detected '{'MOL', 'UNL'}'

ERROR: verify your input file 'mol_att.mol2'. Aborting ...

The input file for this attempt is attached to the post and named "mol_att.mol2". It is puzzling, since there is no MOL named residue. After some investigation the @UNITY_ATOM_ATTR section was an issue, it is wrongly interpreted and converted into dummy atoms of newly created MOL residue. In next attempts

I tried to delete invalid fragment and run Acpype again, input file: “mol_noatt.mol2”. It gave me generated topology, but after minimization using parameters from em.gro the output was a distorted molecule.

Is the problem with absence of the attributes section or there is another issue in my molecule that I did not spot?

Best regards.