Hello users: I am facing the error in energy minimization step performed on system_inflated.gro, after system inflation step in a membrane protein simulation with ligand.

My system_inflated.gro is okay. Then i ran the next command:

gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr

and i received the error:

WARNING 1941 [file ffG54a7nb.itp, line 4050]:
Overriding LJ-14 parameters.

old: 0.0102328 2.39177e-05 0.0102328 2.39177e-05
new: SI CHTFE 1 1.023281E-02 2.391775E-05

WARNING 1942 [file ffG54a7nb.itp, line 4052]:
Overriding LJ-14 parameters.

old: 0.00848659 1.73666e-05 0.00848659 1.73666e-05
new: SI CUrea 1 8.486588E-03 1.736663E-05

WARNING 1943 [file ffG54a7nb.itp, line 4054]:
Overriding LJ-14 parameters.

old: 0.00702942 9.36405e-06 0.00702942 9.36405e-06
new: SI NUrea 1 7.029424E-03 9.364055E-06

Generated 1050 of the 3486 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type ‘Protein’
Excluding 3 bonded neighbours molecule type ‘DPPC’
Excluding 3 bonded neighbours molecule type ‘WXG3’

NOTE 2 [file topol.top, line 23875]:
System has non-zero total charge: 6.000000
Total charge should normally be an integer. See
Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation
for discussion on how close it should be to an integer.

Warning: atom name 3789 in topol.top and system_inflated.gro does not match (C1 - H12)
Warning: atom name 3790 in topol.top and system_inflated.gro does not match (C2 - C13)
Warning: atom name 3791 in topol.top and system_inflated.gro does not match (C3 - C12)
Warning: atom name 3792 in topol.top and system_inflated.gro does not match (N4 - H11)
Warning: atom name 3793 in topol.top and system_inflated.gro does not match (C5 - S)
Warning: atom name 3794 in topol.top and system_inflated.gro does not match (C6 - C11)
Warning: atom name 3795 in topol.top and system_inflated.gro does not match (O7 - C14)
Warning: atom name 3796 in topol.top and system_inflated.gro does not match (P8 - H13)
Warning: atom name 3797 in topol.top and system_inflated.gro does not match (O9 - C10)
Warning: atom name 3798 in topol.top and system_inflated.gro does not match (O10 - O)
Warning: atom name 3799 in topol.top and system_inflated.gro does not match (O11 - C)
Warning: atom name 3800 in topol.top and system_inflated.gro does not match (C12 - H)
Warning: atom name 3801 in topol.top and system_inflated.gro does not match (C13 - C1)
Warning: atom name 3802 in topol.top and system_inflated.gro does not match (O14 - H1)
Warning: atom name 3803 in topol.top and system_inflated.gro does not match (C15 - C2)
Warning: atom name 3804 in topol.top and system_inflated.gro does not match (O16 - H2)
Warning: atom name 3805 in topol.top and system_inflated.gro does not match (C17 - H3)
Warning: atom name 3806 in topol.top and system_inflated.gro does not match (C18 - C3)
Warning: atom name 3807 in topol.top and system_inflated.gro does not match (C19 - H4)
Warning: atom name 3808 in topol.top and system_inflated.gro does not match (C20 - H5)
(more than 20 non-matching atom names)

WARNING 1944 [file topol.top, line 23875]:
6081 non-matching atom names
atom names from topol.top will be used
atom names from system_inflated.gro will be ignored

Removing all charge groups because cutoff-scheme=Verlet
Analysing residue names:
There are: 361 Protein residues
There are: 122 Other residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Number of degrees of freedom in T-Coupling group rest is 29604.00

NOTE 3 [file minim_inflategro.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.

This run will generate roughly 1 Mb of data

There were 3 notes

There were 1944 warnings

Program: gmx grompp, version 2018.1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2406)

Fatal error:
Too many warnings (1944).
If you are sure all warnings are harmless, use the -maxwarn option.

if i use maxwarn for all warnings, then i found breakage in my lipid bilayer in system_inflated_em.gro file.

I am following tutorial by Justin Lemkul kalp15 in dppc: KALP-15 in DPPC

I have build ligand topology using ATB builder.

If anyone can help with this, thanks in advance.