[gmx-users] how to solve a fatal error

[Mark Abraham]

Hi,

Sounds like your mutated residue has a name that is not one supported by
the forcefield, so you will need to explore the force field files to see if
there is a way to name it suitably.

Mark

On Sun, Jul 29, 2018, 17:03 Mohammad Goodarzi <mohammad.godarzi at gmail.com>
wrote:

> 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
> --
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