I am performing a protein-ligand MD simulation with GROMACS using the CHARMM forcefield. The ligand was parameterized using cgenff. However, while using the grompp command, I encountered errors regarding the ligand input file (ligand.itp) with error messages "No default Bond Types", "No default U-B Types", etc. How can this problem be solved?
I would really appreciate your suggestion(s).
A screenshot of the error has been attached herewith.
Create a force field file with the parameters generated by cgenff and include it.
There could be several reasons, a few that come to mind:
A. The parameters given by CGenFF are incomplete or you modified the .itp file somehow and they are incomplete.
B. The order of your molecule type in the structure file is different from the order in your topology file.
C. You did not include your ligand's .itp file in your topology file or you included it in a different order than in the structure file.
- Badges
- Science topic
- Similar topics
- Filing