[gmx-users] how to solve a fatal error

[Mohammad Goodarzi]

Fatal Error I got

Basically I am using the following command line

gmx pdb2gmx -f proteinA.pdb -o conf.pdb

Then I selected 20 as follows:

20: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

Then I selected 1 as it was recomended

 1: TIP4P  TIP 4-point, recommended

But I got the following error.

Fatal error:

The residues in the chain MET-1--DIO3332 do not have a consistent type. The

first residue has type 'Protein', while residue BR3330 is of type 'Ion'.

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.

The protein I work with is only chain A of
https://www.rcsb.org/structure/2J3S . I removed the water, chain B from the
file. I mutated one amino acid and saved it in PDB by pymol.

Can anyone tell me what is wrong and how I should solve the issue?

Many thanks