Answers are grounded in this paper and cite their sources.
Tutorial demonstrates preparation of a protein-ligand complex using AMBER parameters, highlighting utility of Viparr.
This tutorial partially copies steps from How to Assign CHARMM Parameters to Desmond-generated System with viparr4 but differs in the parametrization steps. You can use the Schrödinger software suite to prepare systems for molecular dynamics simulations, however, only the OPLS _2005 and OPLS4 force fields can be automatically assigned. This tutorial will show you how to use Desmond with third-party force fields like AMBER, using the Viparr utility from D.E. Shaw Research. You will prepare a protein-ligand complex, generate custom AMBER parameters for the ligand, and use the Viparr utility to convert the generated AMBER parameters into a viparr-formatted template, that can be used for simulations. You can find the input files for this tutorial here:
No takes yet. Share an insight, caveat, or question.
Mast et al. (2021) studied this question.
Synapse has enriched 8 closely related papers on similar clinical questions. Consider them for comparative context: