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 topol.top, line 26]:
** The following macros were defined in the ‘define’ mdp field with the -D**
** prefix, but were not used in the topology:**
** DIHRES_FC**
** DIHRES**
** 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 topol.top -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 “topol.top”?
If so how?
Best regards
Atilio