System has non-zero total charge: 0.000200 You are using a plain Coulomb cut-off, which might produc

[shivam1]

Sorry for the confusion. I have found the similar issue so I have posted it there.
Please have a look.

Fatal error: There were 2 errors in input file(s)

You probably forgot to #include the associated parameter file. If there are new parameters for the ligand, the server generates them and our conversion utility writes them to a separate file. This is addressed in my tutorial: Protein-Ligand Complex