GROMACS version: 2020.2

GROMACS modification: No

I used the LigParGen from Jorgensen’s group to parameterize a small neutral organic ligand. Addition of the ligand to topology with the corresponding reference to its .itp and .prm (contains only atomtypes) introduces a non-integer charge. As a result I have a +0.0004 charge after neutralization. My energy minimization job ran successfully but I had to overwrite the warning about the charge. Is this an acceptable charge to be ignored for md jobs?

–Mike

Floating-point rounding error. Double check that the charges actually sum to zero in the topology.

There is a non-integer charge in the topology (-7.9996). This happens when I add the neutral ligand. As a result, after adding ions to neutralize the charge is 0.0004.

–Mike

This must be the way LigParGen parameterized the ligand. Is this close enough to zero so it can be ignored?

–Mike

Likely. So you’re saying when you add them up yourself (not grompp) you get -7.9996?

Got you. Yes, there is a 0.0004 charge in the ligand topology which should be zero because its a neutral molecule.

Then that is an actual topology error that needs to be corrected.