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update readme #187

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Feb 10, 2023
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update readme #187

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9 changes: 3 additions & 6 deletions README.md
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Expand Up @@ -5,13 +5,12 @@ pAPRika is a toolkit for setting up, running, and analyzing free energy molecula
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# Contributors
- Niel Henriksen (UCSD, Atomwise Inc.)
Expand All @@ -26,9 +25,7 @@ We recommend installing pAPRika in a fresh `conda` environment if possible. Ther

1. The latest release on `conda-forge`:
1. `conda install -c conda-forge paprika`
2. To use all features of pAPRika, you must either have [AmberTools](http://ambermd.org/AmberTools.php) in your `$PATH` or separately install AmberTools with `conda install -c conda-forge ambertools=22`.
3. To use OpenMM features: `conda install -c conda-forge openmm`.
4. To use Plumed restraints: `conda install -c conda-forge plumed`
2. To use all features of pAPRika, you must either have [AmberTools](http://ambermd.org/AmberTools.php) in your `$PATH` or separately install AmberTools with `conda install -c conda-forge ambertools`.

2. The master branch on GitHub:
1. Clone this `git` repository, then inside the `paprika` directory:
Expand All @@ -46,7 +43,7 @@ We recommend installing pAPRika in a fresh `conda` environment if possible. Ther

# Example

In this example, we will setup and simulate butane (BUT) as a guest molecule for the host [cucurbit[6]uril](https://en.wikipedia.org/wiki/Cucurbituril) (CB6). CBs are rigid, symmetric, cyclic host molecules with oxygen atoms around the portal edge of the cavity. We will run the simulation in implicit solvent, using the [Generalized-Born](https://en.wikipedia.org/wiki/Implicit_solvation#Generalized_Born) model, for speed and simplicity, using AMBER. This tutorial assumes familiarity with basic MD procedures.
In this example, we will configure and simulate butane (BUT) as a guest molecule for the host [cucurbit[6]uril](https://en.wikipedia.org/wiki/Cucurbituril) (CB6). CBs are rigid, symmetric, cyclic host molecules with oxygen atoms around the portal edge of the cavity. We will run the simulation in implicit solvent, using the [Generalized-Born](https://en.wikipedia.org/wiki/Implicit_solvation#Generalized_Born) model, for speed and simplicity, using AMBER. This tutorial assumes familiarity with basic MD procedures.

The `cb6-but` folder referred to below are located in the directory `paprika/data`.

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