LigParGen Parameterized Ligand for OPLS-AA/M Introduces a Non-integer Charger

User discussions
1

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

2

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

3

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

4

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

–Mike

5

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

6

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

7

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