Fatal error while doing MD simulation in gromacs related to residuetypes.dat

Question

[Tiara]

Hello everyone, I am new in MD and while doing simulation the gromacs showing "Fatal error: The residues in the chain VAL136--PRO715 do not have a consistent type. The first residue has type 'Protein', while residue ALY685 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. how to solve this error in MD."

I installed gromacs in linux through dirty installation. I tried to find the residuetypes.dat file but couldn't find it. Can anyone help me how to get access and make changes within the file. Thank you

Answer 1

[Mensur Dlakic]

ALY is not a standard amino acid, but rather an acetylated lysine. You can try to add this residue to GROMACS (see the Google search here) or remove the acetyl group (-COCH3) from your PDB file and change the residue type from ALY to LYS. That might work.