I've finished processing phosphorylation on the protein model using the PyTMs plugin in PyMOL. I've tried various methods, but I get the fatal error below on pdb2gmx. Is there a solution?
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Program: gmx pdb2gmx, version 2023.2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 1042)
Fatal error:
The residues in the chain MET1--ASP863 do not have a consistent type. The
first residue has type 'Protein', while residue TPO395 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.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
The solution is also provided in the error:
"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."
Most of the forcefields have parameters for regular/standard (e.g. STY) modified amino acid residues, and they can recognize the modification. If your amino acid is not among them, you need to add the modified residue in the file "residuetypes.dat". You can open this file and see all the standard residues are written there. Create a backup copy, and then edit your desired residue.
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