There is a bug that occurs when a model has the following features:
1) A molecule in the top file is defined once and multiple copies are present in the system. Under the system directive, something along the lines of "molecule 5" if there are five molecules with potentials defined by "molecule"
2) more than one atom type appears in the molecule
In this case, the atom types are mis-assigned internally, which can affect the nonbonded params and bonded params, if they are based on atom type matching.
This bug was missed, since this can not happen with force fields generated directly with SMOG 2. When the force field is generated directly with SMOG 2, these conditions are never satisfied, since there is not currently a tool that will use this convention. Rather, SMOG 2 always treats the biomolecular system as a single molecule, in terms of gromacs top conventions.
Whitford
commented
1 year ago
There is a bug that occurs when a model has the following features: 1) A molecule in the top file is defined once and multiple copies are present in the system. Under the system directive, something along the lines of "molecule 5" if there are five molecules with potentials defined by "molecule" 2) more than one atom type appears in the molecule
In this case, the atom types are mis-assigned internally, which can affect the nonbonded params and bonded params, if they are based on atom type matching.
This bug was missed, since this can not happen with force fields generated directly with SMOG 2. When the force field is generated directly with SMOG 2, these conditions are never satisfied, since there is not currently a tool that will use this convention. Rather, SMOG 2 always treats the biomolecular system as a single molecule, in terms of gromacs top conventions.