Issues Running GROMACS with Amber Force Field - Seeking Guidance

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Dear GROMACS Community,

I hope this message finds you well. I’ve been successfully running simulations with the CHARMM force field but have recently started working with the Amber force field (AMBER99SB-ILDN for proteins and AMBER9 for nucleic acids) and have encountered some difficulties.

Here’s a summary of my process:

  1. Ligand Topology Generation: I used ACPYPE to generate topology files for my ligand, which resulted in .inpcrd, .frcmod, and .prmtop files.
  2. Conversion to GROMACS Format: I converted these files to .gro and .top formats using the following command:
acpype -p LIG_AC.prmtop -x LIG_AC.inpcrd

Incorporating Ligand Topology**: I included the ligand topology in my .top file with:

#include "LIG.top"

Complex Preparation**: I created the ligand-protein complex and proceeded with box generation, solvation, and ion addition.

However, during this process, I encountered the following errors:

ERROR 1 [file LIG.top, line 5]: Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)
ERROR 2 [file LIG.top, line 9]: Incorrect number of atomtypes for dihedral (4 instead of 2 or 4)

These errors suggest issues with the dihedral parameters in the ligand topology file.

Questions:

Could you guide me on the correct steps to resolve these errors?
Is it acceptable to use CHARMM for ligand-protein interactions in terms of data quality, or should I continue trying to resolve the issues with Amber?
Any advice or direction you can provide would be greatly appreciated.

Thank you in advance for your help!

Best regards,

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It’s strange that lines 5 and 9 of your ligand topology would have dihedral entries (these are usually at the end). It would help to see the contents of your LIG.top.