Tried to create a topology file for protein+DNA complex using CHARMM36 ff in Gromacs 2020.3.
When i am running the commands the following error is occurred -:
gmx pdb2gmx -ignh -f Complex.pdb -o complex_processed.gro -water spce
Fatal error:
The residues in the chain T1--A40 do not have a consistent type. The first residue has type 'Other', while residue C2 is of type 'RNA'. 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.
Kindly help, thanks for your anticipation.
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