Force-Field Parameters for Tryptophan Analogues

Published: 30 September 2021| Version 1 | DOI: 10.17632/tbxsb9j8pv.1
Martin Lepsik


AMBER ff99SB-compatible parameters for 7F (TRF) and 7aza (TRN) tryptophan analogues for use in molecular mechanics and molecular dynamics studies


Steps to reproduce

Parameters for the 7FW and 7AzaW residues were obtained by exchanging/deleting the atoms in PyMol (Molecular Graphics System, Version, Schrödinger, LLC), capping the N- and C-termini with acetyl and hydrogen, respectively, and optimizing using the DFT-D3/COSMO method. The potential protonation of the pyridine of 7AzaW was excluded based on the predicted pKa of 3.3 using Chemicalize tool from ChemAxon. Partial atomic charges were derived by the RESP procedure at the HF/6-31G* level. The capping groups were subsequently deleted and the excess charge was dispersed over all the remaining atoms to restore neutrality. The 7FW and 7AzaW residues were assigned AMBER ff99SB force field parameters.


Centre de Recherches sur les Macromolecules Vegetales


Molecular Mechanics with Molecular Dynamics, Molecular Dynamics Study