Usage of GMXLIB

GROMACS version: 2020.2
GROMACS modification: No

Dear all,

I am a little bit confused regarding what can or can’t be done with GMXLIB. I want to simulate a protein-ligand system. I have placed the force field of the ligand in a folder (LIG.itp) and at the beginning of my script I have: export GMXLIB="/my/folder/with/the/force/field".

When I run pdb2gmx it complains that “Residue ‘LIG’ not found in residue topology database” and I should add it to residuetypes.dat. However, as far as I know, in residuetypes.dat we can only have Protein/DNA/RNA/Water/Ions. Is there a way to have pdb2gmx working with a new ligand? Would there be some intrinsic problem if I were to write in residuetypes.dat that LIG is from a Protein type? Would it be possible to allow another category such as “Other” or “Ligand” in residuetypes.dat?

(If I run pdb2gmx on only the protein, then add the coordinate of the ligands and add the .itp to the top file, everything is working, but I was hoping that I could simplify the protocol).

Thank you for your help


The error means there is no .rtp entry for anything called LIG. It is not related to residuetypes.dat, which is used only in determining chains of biopolymers. You can’t provide a LIG.itp as input to pdb2gmx, you need to build an .rtp entry if you want to automate the topology generation process.