Introduction

ANMD [CM22] is a simple conformers generation algorithm that explores motions along single ANM modes. The normal mode calculation is only performed once and a set of structures along each of the first few modes is subjected to energy minimization with OpenMM [E17], producing physically reasonable conformers near the initial energy well. A key feature of ANMD is that each successive mode is sampled with a lower amplitude related to its frequency.

This tutorial demonstrates how to use ANMD to explore the first two modes of a metabotropic glutamate receptor N-terminal domain (PDB id: 1ewk).

Required Programs

The latest versions of ProDy, OpenMM, and PDBFixer are required for ANMD.

Getting Started

We recommend that you will follow this tutorial by typing commands in an IPython session, e.g.:

$ ipython

or with pylab environment:

$ ipython --pylab

First, we will make necessary imports from ProDy, NumPy, and Matplotlib packages.

In [1]: import numpy as np

In [2]: import matplotlib.pyplot as plt

In [3]: from prody import *

In [4]: plt.ion()

We have included these imports in every part of the tutorial, so that code copied from the online pages is complete. You do not need to repeat imports in the same Python session.

How to Cite

If you benefited from ANMD in your research, please cite the following paper:

[CM22]

Mary Hongying Cheng, James M Krieger, Anupam Banerjee, Yufei Xiang, Burak Kaynak, Yi Shi, Moshe Arditi, Ivet Bahar. Impact of new variants on SARS-CoV-2 infectivity and neutralization: A molecular assessment of the alterations in the spike-host protein interactions, iScience 2022 25(3):103939.

Additionally, please also cite the following paper for OpenMM:

[E17]

Eastman P., et al. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics, PLoS Comput Biol 2017 13:e1005659.