[gmx-users] HELP - Fatal error gmx pdb2gmx

Justin Lemkul jalemkul at vt.edu
Sat May 11 00:00:22 CEST 2019

On 5/10/19 2:26 PM, Edjan Silva wrote:
> I deleted all non-protein molecules and saved the file. I typed the
> following command:
> *gmx pdb2gmx -f 4gy7.pdb -o conf.gro -ignh*
> The error was as follows:
> *Fatal error:*
> *The residues in the chain MET1--PHE840 do not have a consistent type. The*
> *first residue has type 'Protein', while residue CME59 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
> *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.*
> *For more information and tips for troubleshooting, please check the
> *website at http://www.gromacs.org/Documentation/Errors
> <http://www.gromacs.org/Documentation/Errors>*
> I could not run the command without problem. What should I do?

Have you tried following what the error says by adding the nonstandard 
residue to residuetypes.dat?



Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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