I am able to generate the parameter topology files for protein and water box using TINKER but am not able to generate these for my ligand as it is finding no atom types and atom class in TINKER. I'll appreciate any minor suggestion.
you need to parameterize the ligand with "Poltype" . follow the details given here:
Poltype:Poltype - tinkergpu (utexas.edu)
Tinkergpu:Tinker-tut - tinkergpu (utexas.edu)
pren/poltype: POLTYPE: AMOEBA parametrization tool (github.com)
Cheers
Zahra
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