Minimization error for appplying amber 96 ff

User discussions
1

GROMACS version: 5.1

Hi all,
I am using the Samson user interface (Because I am not familiar with the necessary syntax in linux) for using GROMACS for setting up the force field during the minimization step, I received the following error.

How do I circumvent this error?

Kindly help

Regards

Warning: Starting residue Gro0 (Ligand) in chain not identified as Protein/RNA/DNA.

Problem with chain definition, or missing terminal residues.

This chain does not appear to contain a recognized chain molecule.

If this is incorrect, you can edit residuetypes.dat to modify the behavior.

2

It says, the molecule you using in your file is not in the type of defined Protein/DNA/RNA.
You need to read gromacs manual even if you work with SAMSON

3

yeah, it is neither a protein nor a nucleic acid. Gro Stands for ligand in the PDB File.

4

pdb2gmx can’t be used for species it doesn’t know. You will have to supply parameters for any unknown species, which is usually something you do with non-GROMACS software.