Gmx grompp error

User discussions
1

GROMACS version: 2020.1
GROMACS modification: Yes/No

I am trying to simulate a detergent-ligand micelle complex generated from Charmm-GUI. However, when I run gmx grompp, I get the following error:

WARNING 1 [file topol.top, line 33]:
The following macros were defined in the ‘define’ mdp field with the -D
prefix, but were not used in the topology:
POSRES_FC_SC
If you haven’t made a spelling error, either use the macro you defined,
or don’t define the macro.

topol.top looks like:

; Include forcefield parameters
#include “toppar/forcefield.itp”
#include “toppar/UNL.itp”
#include “toppar/BDDM.itp”
#include “toppar/SOD.itp”
#include “toppar/CLA.itp”
#include “toppar/TIP3.itp”

[ system ]
; Name
Title

[ molecules ]
; Compound #mols
UNL 1
BDDM 133
SOD 53
CLA 52
TIP3 18760

and minimization.mdp file looks like:

define = -DPOSRES -DPOSRES_FC_BB=4000.0 -DPOSRES_FC_SC=2000.0 -DPOSRES_FC_LIPID=1000.0 -DDIHRES -DDIHRES_FC=1000.0
integrator = steep
emtol = 1000.0
nsteps = 5000
nstlist = 10
cutoff-scheme = Verlet
rlist = 1.2
vdwtype = Cut-off
vdw-modifier = Force-switch
rvdw_switch = 1.0
rvdw = 1.2
coulombtype = PME
rcoulomb = 1.2
;
constraints = h-bonds
constraint_algorithm = LINCS

Any ideas?

2

Remove the specification of -DPOSRES_FC_SC from the define line, since it is apparently unused by the topology.