Hi, I'm trying to do a simulation of my docking results and i got this error
Fatal error:
The residues in the chain MET1--NI602 do not have a consistent type. The first
residue has type 'Protein', while residue KCX219 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 have tried adding residue name to residuetypes.dat and also added the residue to the forcefield at the aminoacids.rtp file based on previous papers but i'm still getting the error. perhaps im doing it wrong. in the residuetypes.dat i put KCX Protein but i still get the error as 'Other'. Where should i change the residue type? or is it because i put the wrong residue type?
anyone know how to solve this?
You can use openforcefield to add a residue to a forcefield:
https://github.com/openforcefield/openfftoolkit/tree/master/examples#examples-using-smirnoff-with-the-toolkit.
If you want to perfomed a protein-ligand complex simulation follow GROMACS tutorial:
http://www.mdtutorials.com/gmx/complex/index.html
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