HI,
I should like to adapt the “Protein MD Setup tutorial using BioExcel Building Blocks” workflow
to the protein of my concern including the Zn and Mg ions present in the solved structure.
HI,
I should like to adapt the “Protein MD Setup tutorial using BioExcel Building Blocks” workflow
to the protein of my concern including the Zn and Mg ions present in the solved structure.
I have used different ff ( amber99, amber99sd, amber99sd-idln ,oplsaa ).
The problem is that I receive the following:
“Fatal error:
The residues in the chain ALA1–ZN202 do not have a consistent type. The first
residue has type ‘Protein’, while residue ZN201 is of type ‘Ion’. 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.”
The solved structure has two chains.
The error is for the first chain having only Zns coordinated
by 4 Cys and 3 Cys and 1 His for the first and second ion respectively.
The second chain has two Zns, coordinated by Cys and His and one MG.
My concern is for the MG that is coordinated by an Asp and Glu in an active site.
Some papers refer that the previous residues together with other two Asp and Glu are catalytic residues.
I am new to GROMACS.
Any suggestions to make the MD simulation with the two chains with their ions?
Thanks.
Saverio