Are newer AMBER force fields compatible with GROMACS?

User discussions
1

GROMACS version: 2023.2
GROMACS modification: No
I realized that the AMBER force fields that GROMACS currently has implemented are kind of dated. I downloaded the AMBER14SB force field from User contributions — GROMACS webpage https://www.gromacs.org documentation but when I created my ions.tpr file I got these errors

ERROR 1 [file topol_Protein_chain_A.itp, line 127581]:
  No default Per. Imp. Dih. types


ERROR 2 [file topol_Protein_chain_A.itp, line 127871]:
  No default Per. Imp. Dih. types


ERROR 3 [file topol_Protein_chain_A.itp, line 128121]:
  No default Per. Imp. Dih. types


ERROR 4 [file topol_Protein_chain_A.itp, line 128129]:
  No default Per. Imp. Dih. types


ERROR 5 [file topol_Protein_chain_A.itp, line 128183]:
  No default Per. Imp. Dih. types


ERROR 6 [file topol_Protein_chain_A.itp, line 128198]:
  No default Per. Imp. Dih. types


ERROR 7 [file topol_Protein_chain_A.itp, line 128425]:
  No default Per. Imp. Dih. types


ERROR 8 [file topol_Protein_chain_A.itp, line 128650]:
  No default Per. Imp. Dih. types


ERROR 9 [file topol_Protein_chain_B.itp, line 27951]:
  No default Per. Imp. Dih. types

I don’t know if this a problem with the force field itself or GROMACS. Also can you install Ambertools, find the force field folder and move them over to GROMACS same way you can use the CHARMM36 force field or am I missing a step?

2

User contributions have undergone no formal validation; use at your own risk. You’ll run into issues like this.

A big one :) You have to convert the native force field files into GROMACS format. That’s a rather huge undertaking, one that we’ve been refining and overhauling for years to ensure compatibility of CHARMM in GROMACS. It would not be a trivial task to port over an AMBER parameter set properly. Clearly, people have tried and had some success, but problems do arise.

3

Hi, just now I’m working on an automated workflow to read Amber files/parameter sets and write them as Gromacs .ff directories. I could already validate it against Gromacs energies with ff99, 99sb, 99sb-ildn and ff03. Feel free to get in touch at milosz.wieczor@irbbarcelona if you want to try it out with one of the latest Amber FFs before I make a more official release.