Macros not used in the topology

GROMACS version: 2021.1
GROMACS modification: No

Dear all,

I have created my ligand/protein complex with CHARMM-GUI. The tgz file contains the same files as described by [Amo1997] in the topic discussion of Aug/2020.

While minimizing my protein/ligand complex I ran into the following warning:

WARNING 1 [file, line 26]:
** The following macros were defined in the ‘define’ mdp field with the -D**
** prefix, but were not used in the topology:**
** If you haven’t made a spelling error, either use the macro you defined,**
** or don’t define the macro**

The command I used is:
gmx grompp -f step5.0_minimization.mdp -o em.tpr -c step4_input.gro -r step4_input.gro -p -n index.ndx -maxwarn -1

Although I manage to end up the equilibration step, the warning persists:

NOTE 1 [file step5.0_minimization.mdp]:
** Removing center of mass motion in the presence of position restraints**
** might cause artifacts. When you are using position restraints to**
** equilibrate a macro-molecule, the artifacts are usually negligible**.

How could I add DIHRES_FC and DIHRES definitions in topology?
How can I interpret this warning?
Is it a matter of adding DIHRES_FC and DIHRES definitions in the topology file “”?
If so how?

Best regards

this conversation may help you to understand the [NOTE]

1 Like

Dea Alessandra,
Thank you for directing me to this link. I think I now understand the issue.
Best regards