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

Patel, Hershna h.patel28 at herts.ac.uk
Fri Apr 28 17:41:17 CEST 2017

?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.?



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