Is there anyone who can help me parameterizing theligand molecule with AMOEBA polarizing force field for using it in AMBER?

Shakir Ali Siddiqui @Shakir-Ali-Siddiqui

18 December 2020 1 5K Report

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.

Zahra Aliakbar Tehrani

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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