Developing Nonstandard Parameters
The following tutorials give examples on how to parameterize systems that
are complicated. For standard parameters, please see the Force Field page.
Simulating a pharmaceutical compound using antechamber and the Generalized Amber Force Field
Antechamber is a set of tools in Amber that
can be used to prepare input files for organic molecules, which can then be
read into LEaP and used to create prmtop and inpcrd files. The Antechamber
suite is designed for use with the
General
AMBER Force Field (GAFF) and is ideal for setting up
simulations involving organic pharmaceutical compounds or other organic
molecules. In this tutorial we will use antechamber to create a leap input
file for BMS's HIV reverse transcriptase inhibitor sustiva (efavirenz). Then
we set up a simulation of sustiva bound to HIV-RT.
Japanese
translation) By Ross Walker and Sishi Tang.
Original antechamber tutorials
These are a set of original antechamber tutorials. They contain examples of how to generate topology files for normal molecules, non-standard amino acid resues, and nucleotides in gas simulations.
Setting up a
DNA-Ligand System
This tutorial covers setting up an advanced system. In this case it shows you
how to set up a dye system that is covalently bound to DNA. It also includes
manually running multiconformational RESP fits, building custom units and
assigning parameters manually. By Bryan Leland, David Paul, Brent Krueger and Ross
Walker.
Simulating the Green Fluorescent Protein and building a modified amino acid residue
This tutorial prepares a system with a modified amino acid. It differs from other examples that parametrize small organic compounds
because the custom residue is part of a
polymer chain. By Jason Swails, Dave Case, and Tai-Sung Lee.
Metal Ion Modeling
Tutorial
In this tutorial we will delineate several
modeling strategies of metal ions in mixed systems (proteins and nucleic
acids) using the AmberTools package. Both the bonded model and nonbonded
model are illustrated. For the bonded model, MCPB and MCPB.py are used to
facilitate the modeling. While for the nonbonded model modeling strategies
for the 12-6 Lennard-Jones (LJ) and 12-6-4 LJ-type nonbonded models are
presented. (Japanese
translation) By Pengfei Li and Kenneth M. Merz Jr.
Electrostatic Parameterization with PyRESP
In this tutorial we will
understand the limitations of additive force fields and the need for polarizable models like pGM-ind and pGM-perm. Then this tutorial will show you the steps involved in the parameterization process of the PyRESP algorithm.
Deriving Implicitly Polarized Charges in mdgx
This example will guide users through the process of making implicitly
polarized charges for glycerol, appropriate for simulations in liquid water. This
functionality in the mdgx program offers a self-contained and
highly adapatable way for users to create charges tailored for specific
environments and understand the level of accuracy. The same procedures that
make IPolQ
charges can be leveraged to perform traditional ESP fitting.
By David S. Cerutti.
Deriving custom force field parameters with
mdgx
This example showcases the mdgx valence parameter fitting
capabilities, taking the glycerol from the previous tutorial and also
including a more complicated diol. Parameters are derived in a streamlined,
highly automated procedure that puts users firmly in control of the molecular
model building. Generational learning improves the outcome and ensures that
the model can guide simulations while maintaining agreement with its quantum
benchmark. By David S. Cerutti.
Adding custom extra points to a model
This example showcases an expanded extra point palette debuted in Amber22. Models enhanced
with customized extra points will run in either pmemd or pmemd.cuda
based on topologies modified by mdgx. More accurate electrostatic and hydrogen
bonding models are within reach of Amber simulations. By David S. Cerutti.
Deprecated
Building
your own Custom Residues (old version)
This tutorial is somewhat replaced
by the tutorials directly above and below. However, it is kept here since it
shows our original method for creating a system containing nonstandard
residues, in this case a metal atom. A new unit is generated in
xleap in order to simulate the plastocyanin system with a
bound
copper ion.
There are two versions of this tutorial. The first is a
simple version which creates
just a new copper residue and approximates it as a +1 ion. There is also a
more advanced version where
new special histidine and methionine residues are created so that different
charges and bond / angle and dihedral parameters
can be used. By Ross Walker.
[Deprecated] Generating Force
Field Parameters with Paramfit
In this tutorial we will generate force field parameters for two small
molecules from ab-initio quantum calculations using the AmberTools
program Paramfit. This tutorial generates the phi and psi dihedral potentials
over two different small peptide chains, and details each step of the
parameter generation process from preparation of a conformational sampling of
each structure to generation of quantum data to evaluating the quality of the
resulting parameters. By Robin M. Betz.
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