I am trying to generate topology file in GROMACS for an enzyme (PDB code =1HBN). But I encountered the following error.
Fatal error:
"The residues in the chain ALA2--ALA549 do not have a consistent type. The
first residue has type 'Protein', while residue MHS257 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."
Can anyone please kindly help me to solve this.
Firstly, check your 1HBN.pdb in textual editor. You have this line:
MHS D 257 HIS N1-METHYLATED HISTIDINE
So, the MHS cannot be processed by standard force field because there is no such aminoacid.
Secondly, you need to deal with it. You can manually add MHS in the selected forcefield or if you don't need your histidine to be N1-methylated you can remove methyl from N1-atom. There are some ways but I tried to delete non-desired atoms from PyMol interface and then rename MHS to HIS in .pdb file (open it via textual editor and just replace MHS -> HIS).
I hope this will work for you.
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