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

User discussions
1

GROMACS version: 2018.1
Here post your question :
i m trying to run the command: gmx pdb2gmx -f 2n0a.pdb -o 2n0a_processed.gro -ignh
i am using the force field: charm 36-july 2022
water model that is opted is TIP4P.
whenever i am running this command error shows up:
Program: gmx pdb2gmx, version 2018.1
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1149)

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

i tried the same command with charm 36-ff feb 2021 and charm-ff 36 july 2021. that does not show any error.
why is it only showing error in charm 36-ff 2022??

2

Choose appropriate termini interactively, as explained here: Newest CHARMM36 port for GROMACS - #11 by jalemkul

3

Here, can we assume that the structure of protein isn’t repaired for missing loops properly by chimera web modeller service ?

4

The error referred to in this thread has nothing to do with the integrity of a model produced by any software. It’s purely due to a quirk in patch naming in CHARMM that GROMACS doesn’t interpret correctly. If you have an N-terminal MET residue, you MUST interactively select termini to write the topology.