Atom C1 not found in building block (pdb2gmx fatal error)

User discussions
1

GROMACS version: 2022.2-spack
GROMACS modification: No

I have been trying to reproduce the Protein-Ligand Complex Tutorial (Protein-Ligand Complex). However, when I use the command “gmx pdb2gmx - f 3HTB_clean.pdb -o 3HTB_processed.gro” a fatal error appears: “atom C1 not found in buiding block 1MET while combining tdb and rtp”.

I’ve tried to add the number “1” to the atoms and I even used the structure provided in the tutorial. But none of my attempts succeed. How can I fix this issue?

Thank you.

2

If you are using the latest (July 2022) C36 port, we have included basically the whole force field, which means more terminal patches that might or might not be relevant. pdb2gmx is matching “MET” from the protein sequence with a terminal patch that should only be applied to carbohydrates. This is something that pdb2gmx tries to be smart about but sometimes fails.

The solution is to manually select appropriate terminal patches with the -ter option.

3

Thank you for explication. However, I didn’t understand how to use -ter option

This is the error

Start terminus MET-1: MET1
End terminus LYS-152: COO-

Program: gmx pdb2gmx, version 2022.3
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1132)

Fatal error:
atom C1 not found in buiding block 1MET while combining tdb and rtp

4

Select the NH3+ patch for the N-terminus (typical for proteins).