Nonstandard residues prep
From Rizzo_Lab
This tutorial is created by and for AMS536 class at Stony Brook University and made available for the use of the whole modeling community.
The following are examples of a work flow of how to assign parameters for non-standard residues compatible with the amber program. This procedure will give you reasonable parameters; however, the charge calculation should use higher levels of theory and the other parameters should be optimized Further perhaps fit to QM or optimizing to reproduce experimental observables. Parameters assigned from gaff.
Fluorophenylalanine
PLEASE ADD DISCRIPTION
non-starandard Nuclaic acids with modified backbone
PLEASE ADD DISCRIPTION
