2 Developing Nonstandard Parameters
2.2 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
2.3 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
2.4 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.
2.5 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
2.6 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
2.7 Adding custom extra points to a model
This example showcases an expanded extra point palette set to debut in Amber22 (contact
the developers for the latest master branch code if you need early access). 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] 2.8 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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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