GROMACS version: 2025.0
GROMACS modification: No
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i am very new to molecular dynamics and protein engineering in general so please bear with me. my goal is to generate the free energy calculations for small regions within the protein to analyze the affect of a substitution, starting with following this tutorial. but i first need to get the .gro file for my protein, where i am stuck. i am trying to run this command to generate the .gro file for MT-COX2 (pdb=5Z62).
gmx pdb2gmx -f 5Z62.pdb -o 5Z62_processed.gro -water spce -missing
i choose force field 9 ( gromacs 43a1), although i’m not 100% sure this is the right choice. anyways, i get this error:
WARNING: WARNING: Residue 79 named PHE of a molecule in the input file was mapped
to an entry in the topology database, but the atom CZ used in
an interaction of type improper in that entry is not found in the
input file. Perhaps your atom and/or residue naming needs to be fixed.
Fatal error:
The residues in the chain CU601–PEE605 do not have a consistent type. The first residue has type ‘Ion’, while residue HEA603 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.
i got this error for mutiple residues. i understand this is a common error but i am confused why this error pops up since these residues are amino acids. i am also not really sure how to edit the .pdb file to make it more compliant with gromacs.
sincerly, a very confused individual. thank you!