Residue 6 named GLU of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
Dear Amaresh Mohanty
You can fix your PDB file by using spdbv software. Simply, import the structure file and use Quick and Dirty fix tool for editing your PDB file. This will handle the problem.
Make sure there are no missing atoms in the input file. If the input file is derived from an X-ray crystal structure, the information about missing atoms is included in the REMARK section. If some side-chains are incomplete or missing, add them, e.g., using PyMOL mutagenesis tool: choose 'no mutation' and carefully, rather than blindly, select a proper rotamer.
Amaresh Mohanty You can energy minimize your protein using Swiss PDB Viewer
https://spdbv.vital-it.ch/.
It will make all necessary changes in atom naming.
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