Addition of AMBER OL3 Force field in GROMACS

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

Command line:

gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water tip3p

Output:

Select the Force Field:
From ‘/usr/local/gromacs/share/gromacs/top’:
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
9: CHARMM36 all-atom force field (February 2026)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

I want to add AMBER OL3 FFs in the option and want to use that. guild me to do so.

2

You need to download ff files from OL Force Field Refinement for RNA and DNA Simulations and then either copy them to your working folder or to [path to your gromacs installation]/share/gromacs/top/ if you plan to use them regularly. Then it should pop up as an option when choosing FF with automatically assigning OL24 to DNA, OL03 to RNA and ff14sb to proteins.

1 Like
3

Thankyou @jindrich.lnenicka