The different bond parameters obtained from LigParGen and from oplsaa.ff in Gromacs

User discussions
1

GROMACS version:2020.3
GROMACS modification: No
Here post your question:I have a small and foolish question. The values I obtained from LigParGen are different to what I get it from oplsaa.ff OPLS-AA force field distributed with GROMACS. Taking ethanol for example, the CT-CT bond obtain from LigParGen is “268.00 1.5290” and the values from the oplsaa.ff is “0.153 2.24e+05”, corresponds to “CT CT 1 0.15290 224262.4; CHARMM 22 parameter file”. I do not know why they are different and how can I correctly use the values obtained from oplsaa.ff. Because many atoms can be identified by TPPMKTOP but not by LigParGen. Can anyone give me some suggestions?
I would be very grateful indeed for any help you could give me.
Best wishes.
Yuanqi

2

The values are the same, just in different units. The force constant from LigParGen is in kcal mol-1 Å-2 (and appears to likely be already expressed as k/2 instead of k, and GROMACS format is kJ mol-1 nm-2, so 268 * 2 * 100 * 4.184 = 224262.4. The reference bond length is simply in Å instead of nm.