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2 Developing Nonstandard Parameters

2.1 Simulating a pharmaceutical compound using antechamber and the Generalized Amber Force Field

sustiva 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

2.2 Setting up a DNA-Ligand System

A1 toc image 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)

A1 old toc image 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

MCPB toc image 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

IPolQ toc image

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

MM vs QM Energy toc image

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

Extra point toc image 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

Paramfit toc image 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

"How's that for maxed out?"

Last modified: Aug 27, 2021