[gmx-users] ERROR atom 'X' has mass 0 (state A) / 0 (state B)

[Patel, Hershna]

?Dear Gromacs users,


When running grompp to create  'ions.tpr' file for energy minimisation of a protein-ligand complex (following the protein-ligand complex tutorial), I am getting the error:


ERROR 1 [file mNEP2.top, line 19069]:
 atom C2 (Res LIG-1) has mass 0 (state A) / 0 (state B)

Atom 3 'C2' in moleculetype 'zinc01509994' is not bound by a potential or constraint to any other atom in the same moleculetype.

I get this error for 12 C atoms of my ligand.


Line 19069 in my .top file is the number of solvent molecules in the [ molecules ] directive.


How do I resolve this, please? I am using Gromacs version 2016, and generated the ligand .itp/.top/.gro files using ACPYPE.?


Regards

Hershna