From 12c42311639caed101a2f02d2447becc08fb9413 Mon Sep 17 00:00:00 2001 From: Peter Eastman Date: Wed, 8 Feb 2023 08:28:25 -0800 Subject: [PATCH] Updated installation instructions (#265) --- Manual.html | 12 +++++++----- README.md | 10 ++++++++++ 2 files changed, 17 insertions(+), 5 deletions(-) diff --git a/Manual.html b/Manual.html index 335ff27..bdd10f0 100644 --- a/Manual.html +++ b/Manual.html @@ -4,7 +4,7 @@

PDBFixer

-
Copyright 2013-2017 by Peter Eastman and Stanford University
+
Copyright 2013-2023 by Peter Eastman and Stanford University

1. Introduction

@@ -28,16 +28,18 @@

1. Introduction

2. Installation

-To install PDBFixer, navigate to the root directory of the source distribution you've download and type +The easiest way to install PDBFixer is with conda or mamba. +

+conda install -c conda-forge pdbfixer +

+Alternatively you can install it from source. Download the repository, navigate to the root directory, and type

python setup.py install

This will install the PDBFixer python package as well as the command line program pdbfixer.

-Before running PDBFixer, you must first install OpenMM 6.3 or later. Follow the installation instructions in the OpenMM manual. It is also recommended that you install CUDA or OpenCL, since the performance will usually be faster than when running on the CPU platform. PDBFixer requires that NumPy be installed. -

-Alternatively, PDBFixer is included as part of the Omnia suite for molecular simulation. If you install the suite, PDBFixer and its dependencies will be included. +Before running PDBFixer, you must first install OpenMM. Follow the installation instructions in the OpenMM manual. It is also recommended that you install CUDA or OpenCL, since the performance will usually be faster than when running on the CPU platform. PDBFixer requires that NumPy be installed. All of these dependencies are included automatically when installing with conda.

3. PDBFixer as a Desktop Application

diff --git a/README.md b/README.md index 6fc6f39..944b361 100644 --- a/README.md +++ b/README.md @@ -15,3 +15,13 @@ PDBFixer is an easy to use application for fixing problems in Protein Data Bank - Build a water box for explicit solvent simulations. See our [manual](https://htmlpreview.github.io/?https://github.com/openmm/pdbfixer/blob/master/Manual.html) + +## Installation + +PDBFixer can be installed with conda or mamba. + +``` +conda install -c conda-forge pdbfixer +``` + +Alternatively you can install from source, as described in the manual. \ No newline at end of file