I want to create a topology for a ligand containing metal centre Cu 2+ which is actually a metal complex. So as suggested in my earlier question i tried to use the mcpb.py tool of AmberTools. But the problem i am facing now is the error in which the software couldnot find the resname in the pdb. I have created my pdb using gaussview where the resname doesnot come. If i manually edit the resname in the pdb of the molecule, it becomes distored in vmd and the Cu atom is recognized as a carbon atom. While performing the mcpb.py i have successfully created the mol2 files for the Cu 2 atom as well as the ligand also the frcmod files. And also combined them into a single pdb file. I have also created the .in file for running the command: MCPB.py -i 1OKL.in -s 1. In this particular step the error shows up as attached in the file. If anyone can suggest some ways to overcome this problem i shall be ever grateful.

Similar questions and discussions