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alanwilter committed Jun 6, 2022
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A tool based in **Python** to use **Antechamber** to generate topologies for chemical
compounds and to interface with others python applications like CCPN and ARIA.

`acpype` is pronounced as ***ace + pipe***
`acpype` is pronounced as **_ace + pipe_**

Topologies files to be generated so far: CNS/XPLOR, GROMACS, CHARMM and AMBER.

Expand Down Expand Up @@ -55,61 +56,64 @@ It was inspired by:
For Non-uniform 1-4 scale factor conversion (e.g. if using **GLYCAM06**), please cite:

> BERNARDI, A., FALLER, R., REITH, D., and KIRSCHNER, K. N. ACPYPE update for
nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER
to GROMACS. SoftwareX 10 (2019), 100241. Doi: [10.1016/j.softx.2019.100241](https://doi.org/10.1016/j.softx.2019.100241)
> nonuniform 1–4 scale factors: Conversion of the GLYCAM06 force field from AMBER
> to GROMACS. SoftwareX 10 (2019), 100241. Doi: [10.1016/j.softx.2019.100241](https://doi.org/10.1016/j.softx.2019.100241)
For `Antechamber`, please cite:
>

> 1. WANG, J., WANG, W., KOLLMAN, P. A., and CASE, D. A. Automatic atom type and
bond type perception in molecular mechanical calculations. Journal of Molecular
Graphics and Modelling 25, 2 (2006), 247–260. Doi: [10.1016/j.jmgm.2005.12.005](https://doi.org/10.1016/j.jmgm.2005.12.005)

> 2. WANG, J., WOLF, R. M., CALDWELL, J. W., KOLLMAN, P. A., and CASE, D. A.
Development and testing of a General Amber Force Field. Journal of Computational
Chemistry 25, 9 (2004), 1157–1174. Doi: [10.1002/jcc.20035](https://doi.org/10.1002/jcc.20035)

If you use this code, I am glad if you cite:

> SOUSA DA SILVA, A. W. & VRANKEN, W. F.
ACPYPE - AnteChamber PYthon Parser interfacE.
BMC Research Notes 5 (2012), 367 Doi: [10.1186/1756-0500-5-367](https://doi.org/10.1186/1756-0500-5-367)
> ACPYPE - AnteChamber PYthon Parser interfacE.
> BMC Research Notes 5 (2012), 367 Doi: [10.1186/1756-0500-5-367](https://doi.org/10.1186/1756-0500-5-367)
and (optionally)

> BATISTA, P. R.; WILTER, A.; DURHAM, E. H. A. B. & PASCUTTI, P. G. Molecular
Dynamics Simulations Applied to the Study of Subtypes of HIV-1 Protease.
Cell Biochemistry and Biophysics 44 (2006), 395-404. Doi: [10.1385/CBB:44:3:395](https://doi.org/10.1385/CBB:44:3:395)
> Dynamics Simulations Applied to the Study of Subtypes of HIV-1 Protease.
> Cell Biochemistry and Biophysics 44 (2006), 395-404. Doi: [10.1385/CBB:44:3:395](https://doi.org/10.1385/CBB:44:3:395)
Alan Silva, DSc

alanwilter *at* gmail *dot* com
alanwilter _at_ gmail _dot_ com

#### How To Use ACPYPE

##### Introduction

We now have an up-to-date *web service* at **[Bio2Byte](http://bio2byte.be/acpype/)** (but it **does not** have the `amb2gmx` functionality).
We now have an up-to-date _web service_ at **[Bio2Byte](http://bio2byte.be/acpype/)** (but it **does not** have the `amb2gmx` functionality).

To run `acpype`, locally, with its all functionalities, you need **ANTECHAMBER** from package
[AmberTools](http://ambermd.org/) and
[Open Babel](http://openbabel.org/wiki/Main_Page) if your input files are of PDB
format.

However, if one wants `acpype` just to emulate *amb2gmx.pl*, one needs nothing
at all but *[Python](http://www.python.org)*.
However, if one wants `acpype` just to emulate _amb2gmx.pl_, one needs nothing
at all but _[Python](http://www.python.org)_.

There are several ways of obtaining `acpype`:

1. Via **[CONDA](https://anaconda.org/search?q=acpype)**:

*(It should be wholesome, fully functional, all batteries included)*
_(It should be wholesome, fully functional, all batteries included)_

```bash
conda install -c conda-forge acpype
```

2. Via **[PyPI](https://pypi.org/project/acpype/)**:

*(Make sure you have `AmberTools` and, optionally but highly recommended, `OpenBabel`)*
_(Make sure you have `AmberTools` and, optionally but highly recommended, `OpenBabel`)_

```bash
# You can use conda to get the needed 3rd parties for example
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pip install git+https://github.com/alanwilter/acpype.git
```

**NB:** If using OpenBabel python module, it's really ***CRITICAL*** to have it installed in the same `Python` environment of `acpype`.
**NB:** If using OpenBabel python module, it's really **_CRITICAL_** to have it installed in the same `Python` environment of `acpype`.
3. By downloading it via `git`:
*(Make sure you have `AmberTools` and, optionally but highly recommended, `OpenBabel`)*
_(Make sure you have `AmberTools` and, optionally but highly recommended, `OpenBabel`)_
```bash
# You can use conda to get the needed 3rd parties for example
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4. Via **[Docker](https://hub.docker.com/repository/docker/acpype/acpype/)**:
*(It should be wholesome, fully functional, all batteries included)*
_(It should be wholesome, fully functional, all batteries included)_
If you have Docker installed, you can run `acpype_docker.sh` by:
Expand All @@ -161,7 +165,7 @@ There are several ways of obtaining `acpype`:
On Windows:
Using Command Prompt:
In the directory where the `acpype_docker.bat` file is found:
In the directory where the `acpype_docker.bat` file is found:
```bash
setx /M path "%path%;%cd%"
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./run_acpype.py -i tests/FFF.pdb
```
It'll create a folder called *FFF.acpype*, and inside it one may find topology
It'll create a folder called _FFF.acpype_, and inside it one may find topology
files for GROMACS and CNS/XPLOR.

Or using a molecule in [SMILES](https://archive.epa.gov/med/med_archive_03/web/html/smiles.html) notation:
Expand All @@ -197,7 +201,7 @@ Or using a molecule in [SMILES](https://archive.epa.gov/med/med_archive_03/web/h
./run_acpype.py -i CCCC # smiles for C4H6 1,3-Butadiene compound
```

It'll create a folder called *smiles_molecule.acpype*.
It'll create a folder called _smiles_molecule.acpype_.
To get help and more information, type:
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#### To Emulate `amb2gmx.pl`
For any given *prmtop* and *inpcrd* files (outputs from AMBER LEaP), type:
For any given _prmtop_ and _inpcrd_ files (outputs from AMBER LEaP), type:
```bash
acpype -p FFF_AC.prmtop -x FFF_AC.inpcrd
```
The output files `FFF_GMX.gro` and `FFF_GMX.top` will be generated inside folder *FFF_GMX.amb2gmx*
The output files `FFF_GMX.gro` and `FFF_GMX.top` will be generated inside folder _FFF_GMX.amb2gmx_
#### To Verify with CNS/XPLOR
At folder *FFF.acpype*, type:
At folder _FFF.acpype_, type:
```bash
cns < FFF_CNS.inp
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