i am new to gromacs. recently i tried to perform protein-ligand MD simulation. during preparation of input file in neutralization section i got following msg
NOTE 2 [file topol.top, line 40852]:
System has non-zero total charge: 0.000100
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.
i searched every possible way to solve this problem but could not find any solution. i have generated ligand prm file from LigParGen and used OPLS AA force field for simulation.
is OPLS AA forcefield is appropriate for protein-ligand simulation?
i have selected OPLS AA force field because SWISSPARAM and CGenFF did not generate prm and itp file for ligand.
thanks in advance
Did you read the page that is linked? You likely don’t have any problem to solve, it’s probably rounding. Double check the charges in the ligand topology to make sure they actually sum to zero (that may be the only real source of excess charge).