Atom N not found in buiding block 1ACE while combining tdb and rtp. How to solve it?

User discussions
1

GROMACS version:2024.2
GROMACS modification: Yes/No
Dear all ,
I’ve tried to perform an MD simulation with a protein-ligand complex. I am using the CHARMM27 FF GROMACS 2024.2 .

When running pdb2gmx it shows me the following error 👇

Fetal error:
“atom N not found in building block 1ACE while combining tdb and rtp”

Can anyone help me to understand what may go wrong?
Thanks in advance …

2

For capped polypeptides, you need to select the appropriate terminal patching (None) with gmx pdb2gmx -ter, otherwise the program tries to build a free amino group onto the acetyl, which is chemically impossible.