luancarvalhomartins
Restraints in ligand.itp file
As the code is written now, the ifdef POSRE_LIG is added to ligand.itp and not to FullSystem.top. I know ligand.itp is included in FullSystem.top, but GROMACS still returns:
"The following macros were defined in the 'define' mdp field with the -D prefix, but were not used in the topology: POSRES_LIG"
If I add the POSRES_LIG line to the topology file, the error is not returned, so I guess prepare_dual_topology.py should add the POSRES_LIG include reference to the topology files and not ligand.itp
Best, Ferran
Sorry it took me a while to reply. And thank you very much for your bug report.
GROMACS should preprocess the input topology file including the ligand.itp contents and correctly recognizing the #ifdef POSRES_LIG there. No warnings should be printed.
Would sharing the complete gmx grompp log? Also, would you mind checking what is the preprocessed topology generated by gmx grompp -pp? It should contain the restraints in case the define = -DPOSRES_LIG is there.
