Fatal error: The residues in the chain ACE47--NMA68 do not have a consistent type. The first residue

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1

GROMACS version:
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Dear Justin,

Hope you all are fine.

Sir, when i am using this
cmd: gmx pdb2gmx -f xx.pdb -o xx.gro -ignh

it shows this fatal error
Fatal error:
The residues in the chain ACE47–NMA68 do not have a consistent type. The
first residue has type ‘Protein’, while residue NMA68 is of type ‘Other’.
Either there is a mistake in your chain, or it includes nonstandard residue
names that have not yet been added to the residuetypes.dat file in the GROMACS
library directory. If there are other molecules such as ligands, they should
not have the same chain ID as the adjacent protein chain since it’s a separate
molecule.

I am using the gmx version 2022.2 and using the GPU system how i will resolve this error.

Secondly, i have tried by adding manually the NAM residue in residuetypes.dat file. Then after run again i am getting this error :-
" Residue type ‘NMA’ not found in residue topology database. "

i have tried from all forcefield… i am using the 4R8T PDB Id.

Could you please help me!

2

NMA is N-methylacetamide in most force fields. If you are trying to apply some kind of C-terminal N-methylamide capping, the appropriate residue name (at least in CHARMM) is NME. I don’t know about other force fields offhand.

3

Thankyou for reply. Could you please tell me! how i do capping. And how i do the gmx pdb2gmx cmd script to clear this fatal error.

4

It seems you’ve already done the capping, you just need to rename NMA in the coordinate file to whatever N-methylamide group your chosen force field expects.