Usage of GMXLIB

User discussions
1

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

Nicolas

2

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.

3

Hello. I am facing a similar problem, Could you please tell more about how can we build an .rtp entry