[gmx-users] how to solve a fatal error
mohammad.godarzi at gmail.com
Sun Jul 29 17:03:09 CEST 2018
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.
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
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
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?
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