# ACPYPE
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## AnteChamber PYthon Parser interfacE
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_**
Topologies files to be generated so far: CNS/XPLOR, GROMACS, CHARMM and AMBER.
**NB:** Topologies generated by `acpype/Antechamber` are based on General Amber Force
Field (GAFF) and should be used only with compatible forcefields like AMBER and
its variant.
Several flavours of AMBER FF are ported already for GROMACS (see [ffamber](http://ffamber.cnsm.csulb.edu/)) as well as to XPLOR/CNS (see [`xplor-nih`](http://ambermd.org/xplor-nih.html)) and [CHARMM](https://www.charmm.org/).
This code is released under **[GNU General Public Licence V3](https://www.gnu.org/licenses/gpl-3.0.en.html)**.
See online [documentation](https://acpype.readthedocs.io/) for more.
### **NO WARRANTY AT ALL**
It was inspired by:
- `amb2gmx.pl` (Eric Sorin, David Mobley and John Chodera)
and depends on `Antechamber` and `OpenBabel`
- [YASARA Autosmiles](http://www.yasara.org/autosmiles.htm) (Elmar Krieger)
- `topolbuild` (Bruce Ray)
- `xplo2d` (G.J. Kleywegt)
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)
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)
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)
Alan Silva, DSc
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).
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)_.
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)_
```bash
conda install -c conda-forge acpype
```
2. Via **[PyPI](https://pypi.org/project/acpype/)**:
If you're using Linux with Intel processors then
```bash
pip install acpype
```
is enough and you should have a complete solution. Oterwise ...
_(Make sure you have `AmberTools` and, optionally but highly recommended, `OpenBabel`)_
```bash
# You can use conda to get the needed 3rd parties for example
conda create -n acpype --channel conda-forge ambertools openbabel
# Or for Ubuntu 20:
apt-get install -y openbabel python3-openbabel libarpack++2-dev libgfortran5
pip install acpype
# or if you feel daring
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`.
3. By downloading it via `git`:
_(Make sure you have `AmberTools` and, optionally but highly recommended, `OpenBabel`)_
```bash
# You can use conda to get the needed 3rd parties for example
conda create -n acpype --channel conda-forge ambertools openbabel
# Or for Ubuntu 20:
apt-get install -y openbabel python3-openbabel libarpack++2-dev libgfortran5
git clone https://github.com/alanwilter/acpype.git
```
**NB:** Using this mode, CHARMM topology files will not be generated.
4. Via **[Docker](https://hub.docker.com/repository/docker/acpype/acpype/)**:
_(It should be wholesome, fully functional, all batteries included)_
If you have Docker installed, you can run `acpype_docker.sh` by:
NOTE: first time may take some time as it pulls the `acpype` docker image.
On Linux / macOS:
```bash
ln -fsv "$PWD/acpype_docker.sh" /usr/local/bin/acpype_docker
```
On Windows:
Using Command Prompt:
In the directory where the `acpype_docker.bat` file is found:
```bash
setx /M path "%path%;%cd%"
```
Commands:
```bash
acpype_docker -i CCCC
acpype_docker -i tests/DDD.pdb -c gas
```
**NB:**
- By installing via `conda` or using via `docker` you get `AmberTools v.21.11` and `OpenBabel v3.1.1`. Our `AmberTools v.21.11` is a stripped version from the original containing only the necessary binaries and libraries and comes with the `charmmgen` binary from `AmberTools17` in order to generate CHARMM topologies.
- By installing via `pip` you get `AmberTools` (as described above) embedded. However, the included binaries may not work in your system (library dependencies issues) and with only provide binaries for Linux (Ubuntu20) and macOS (Intel).
##### To Test, if doing via `git`
At folder `acpype/`, type:
```bash
./run_acpype.py -i tests/FFF.pdb
```
It'll create a folder called _FFF.acpype_, and inside it one may find topology
files for GROMACS and CNS/XPLOR.
Or using a molecule in [SMILES](https://archive.epa.gov/med/med_archive_03/web/html/smiles.html) notation:
```bash
./run_acpype.py -i CCCC # smiles for C4H6 1,3-Butadiene compound
```
It'll create a folder called _smiles_molecule.acpype_.
To get help and more information, type:
```bash
./run_acpype.py -h
```
##### To Install
At folder `acpype/`, type:
```bash
ln -fsv "$PWD/run_acpype.py" /usr/local/bin/acpype
```
Then re-login or start another shell session.
If via `conda` or `pip`, `acpype` should be in your `$PATH`.
##### To Verify with GMX
GROMACS < v.5.0
```bash
cd FFF.acpype/
grompp -c FFF_GMX.gro -p FFF_GMX.top -f em.mdp -o em.tpr
mdrun -v -deffnm em
# And if you have VMD
vmd em.gro em.trr
```
GROMACS > v.5.0
```bash
cd FFF.acpype/
gmx grompp -c FFF_GMX.gro -p FFF_GMX.top -f em.mdp -o em.tpr
gmx mdrun -v -deffnm em
# And if you have VMD
vmd em.gro em.trr
```
##### For MD, do
GROMACS < v.5.0
```bash
grompp -c em.gro -p FFF_GMX.top -f md.mdp -o md.tpr
mdrun -v -deffnm md
vmd md.gro md.trr
```
GROMACS > v.5.0
```bash
gmx grompp -c em.gro -p FFF_GMX.top -f md.mdp -o md.tpr
gmx mdrun -v -deffnm md
vmd md.gro md.trr
```
#### To Emulate `amb2gmx.pl`
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_
#### To Verify with CNS/XPLOR
At folder _FFF.acpype_, type:
```bash
cns < FFF_CNS.inp
```
#### To Verify with NAMD
- see [TutorialNAMD](../../wiki/Tutorial-NAMD)
Raw data
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"description": "# ACPYPE\n\n[](https://GitHub.com/alanwilter/acpype/graphs/commit-activity)<!-- [](https://github.com/ellerbrock/open-source-badges/) -->\n[](https://github.com/alanwilter/acpype)\n[](https://github.com/alanwilter/acpype)\n[](https://github.com/alanwilter/acpype)\n[](https://github.com/alanwilter/acpype)<!--  -->\n[](https://hub.docker.com/r/acpype/acpype)\n[](https://hub.docker.com/r/acpype/acpype/tags)\n[](https://anaconda.org/conda-forge/acpype)\n[](https://anaconda.org/conda-forge/acpype/files)<!--  -->\n[](https://pypi.org/project/acpype/)\n[](https://pypi.org/project/acpype/#files)\n\n[](https://python-poetry.org/)\n[](https://github.com/astral-sh/ruff)\n[](https://github.com/pre-commit/pre-commit)\n[](https://github.com/alanwilter/acpype/commits/master)\n[](https://app.codecov.io/gh/alanwilter/acpype)\n[](https://acpype.readthedocs.io/en/latest/?badge=latest)\n\n\n<!-- [](https://scholar.google.com/citations?view_op=view_citation&hl=en&user=c68TiIUAAAAJ&citation_for_view=c68TiIUAAAAJ:UeHWp8X0CEIC) -->\n\n<!--  -->\n<!--  -->\n\n## AnteChamber PYthon Parser interfacE\n\nA tool based in **Python** to use **Antechamber** to generate topologies for chemical\ncompounds and to interface with others python applications like CCPN and ARIA.\n\n`acpype` is pronounced as **_ace + pipe_**\n\nTopologies files to be generated so far: CNS/XPLOR, GROMACS, CHARMM and AMBER.\n\n**NB:** Topologies generated by `acpype/Antechamber` are based on General Amber Force\nField (GAFF) and should be used only with compatible forcefields like AMBER and\nits variant.\n\nSeveral flavours of AMBER FF are ported already for GROMACS (see [ffamber](http://ffamber.cnsm.csulb.edu/)) as well as to XPLOR/CNS (see [`xplor-nih`](http://ambermd.org/xplor-nih.html)) and [CHARMM](https://www.charmm.org/).\n\nThis code is released under **[GNU General Public Licence V3](https://www.gnu.org/licenses/gpl-3.0.en.html)**.\n\nSee online [documentation](https://acpype.readthedocs.io/) for more.\n\n### **NO WARRANTY AT ALL**\n\nIt was inspired by:\n\n- `amb2gmx.pl` (Eric Sorin, David Mobley and John Chodera)\n and depends on `Antechamber` and `OpenBabel`\n\n- [YASARA Autosmiles](http://www.yasara.org/autosmiles.htm) (Elmar Krieger)\n\n- `topolbuild` (Bruce Ray)\n\n- `xplo2d` (G.J. Kleywegt)\n\nFor Non-uniform 1-4 scale factor conversion (e.g. if using **GLYCAM06**), please cite:\n\n> BERNARDI, A., FALLER, R., REITH, D., and KIRSCHNER, K. N. ACPYPE update for\n> nonuniform 1\u20134 scale factors: Conversion of the GLYCAM06 force field from AMBER\n> to GROMACS. SoftwareX 10 (2019), 100241. Doi: [10.1016/j.softx.2019.100241](https://doi.org/10.1016/j.softx.2019.100241)\n\nFor `Antechamber`, please cite:\n\n> 1. WANG, J., WANG, W., KOLLMAN, P. A., and CASE, D. A. Automatic atom type and\n> bond type perception in molecular mechanical calculations. Journal of Molecular\n> Graphics and Modelling 25, 2 (2006), 247\u2013260. Doi: [10.1016/j.jmgm.2005.12.005](https://doi.org/10.1016/j.jmgm.2005.12.005)\n\n> 2. WANG, J., WOLF, R. M., CALDWELL, J. W., KOLLMAN, P. A., and CASE, D. A.\n> Development and testing of a General Amber Force Field. Journal of Computational\n> Chemistry 25, 9 (2004), 1157\u20131174. Doi: [10.1002/jcc.20035](https://doi.org/10.1002/jcc.20035)\n\nIf you use this code, I am glad if you cite:\n\n> SOUSA DA SILVA, A. W. & VRANKEN, W. F.\n> ACPYPE - AnteChamber PYthon Parser interfacE.\n> BMC Research Notes 5 (2012), 367 Doi: [10.1186/1756-0500-5-367](https://doi.org/10.1186/1756-0500-5-367)\n\nand (optionally)\n\n> BATISTA, P. R.; WILTER, A.; DURHAM, E. H. A. B. & PASCUTTI, P. G. Molecular\n> Dynamics Simulations Applied to the Study of Subtypes of HIV-1 Protease.\n> Cell Biochemistry and Biophysics 44 (2006), 395-404. Doi: [10.1385/CBB:44:3:395](https://doi.org/10.1385/CBB:44:3:395)\n\nAlan Silva, DSc\n\nalanwilter _at_ gmail _dot_ com\n\n#### How To Use ACPYPE\n\n##### Introduction\n\nWe now have an up-to-date _web service_ at **[Bio2Byte](http://bio2byte.be/acpype/)** (but it **does not** have the `amb2gmx` functionality).\n\nTo run `acpype`, locally, with its all functionalities, you need **ANTECHAMBER** from package\n[AmberTools](http://ambermd.org/) and\n[Open Babel](http://openbabel.org/wiki/Main_Page) if your input files are of PDB\nformat.\n\nHowever, if one wants `acpype` just to emulate _amb2gmx.pl_, one needs nothing\nat all but _[Python](http://www.python.org)_.\n\nThere are several ways of obtaining `acpype`:\n\n1. Via **[CONDA](https://anaconda.org/search?q=acpype)**:\n\n _(It should be wholesome, fully functional, all batteries included)_\n\n ```bash\n conda install -c conda-forge acpype\n ```\n\n2. Via **[PyPI](https://pypi.org/project/acpype/)**:\n\n If you're using Linux with Intel processors then\n\n ```bash\n pip install acpype\n ```\n\n is enough and you should have a complete solution. Oterwise ...\n\n _(Make sure you have `AmberTools` and, optionally but highly recommended, `OpenBabel`)_\n\n ```bash\n # You can use conda to get the needed 3rd parties for example\n conda create -n acpype --channel conda-forge ambertools openbabel\n\n # Or for Ubuntu 20:\n apt-get install -y openbabel python3-openbabel libarpack++2-dev libgfortran5\n\n pip install acpype\n\n # or if you feel daring\n\n pip install git+https://github.com/alanwilter/acpype.git\n ```\n\n **NB:** If using OpenBabel python module, it's really **_CRITICAL_** to have it installed in the same `Python` environment of `acpype`.\n\n3. By downloading it via `git`:\n\n _(Make sure you have `AmberTools` and, optionally but highly recommended, `OpenBabel`)_\n\n ```bash\n # You can use conda to get the needed 3rd parties for example\n conda create -n acpype --channel conda-forge ambertools openbabel\n\n # Or for Ubuntu 20:\n apt-get install -y openbabel python3-openbabel libarpack++2-dev libgfortran5\n\n git clone https://github.com/alanwilter/acpype.git\n ```\n\n **NB:** Using this mode, CHARMM topology files will not be generated.\n\n4. Via **[Docker](https://hub.docker.com/repository/docker/acpype/acpype/)**:\n\n _(It should be wholesome, fully functional, all batteries included)_\n\n If you have Docker installed, you can run `acpype_docker.sh` by:\n\n NOTE: first time may take some time as it pulls the `acpype` docker image.\n\n On Linux / macOS:\n\n ```bash\n ln -fsv \"$PWD/acpype_docker.sh\" /usr/local/bin/acpype_docker\n ```\n\n On Windows:\n Using Command Prompt:\n\n In the directory where the `acpype_docker.bat` file is found:\n\n ```bash\n setx /M path \"%path%;%cd%\"\n ```\n\n Commands:\n\n ```bash\n acpype_docker -i CCCC\n\n acpype_docker -i tests/DDD.pdb -c gas\n ```\n\n**NB:**\n\n- By installing via `conda` or using via `docker` you get `AmberTools v.21.11` and `OpenBabel v3.1.1`. Our `AmberTools v.21.11` is a stripped version from the original containing only the necessary binaries and libraries and comes with the `charmmgen` binary from `AmberTools17` in order to generate CHARMM topologies.\n- By installing via `pip` you get `AmberTools` (as described above) embedded. However, the included binaries may not work in your system (library dependencies issues) and with only provide binaries for Linux (Ubuntu20) and macOS (Intel).\n\n##### To Test, if doing via `git`\n\nAt folder `acpype/`, type:\n\n```bash\n./run_acpype.py -i tests/FFF.pdb\n```\n\nIt'll create a folder called _FFF.acpype_, and inside it one may find topology\nfiles for GROMACS and CNS/XPLOR.\n\nOr using a molecule in [SMILES](https://archive.epa.gov/med/med_archive_03/web/html/smiles.html) notation:\n\n```bash\n./run_acpype.py -i CCCC # smiles for C4H6 1,3-Butadiene compound\n```\n\nIt'll create a folder called _smiles_molecule.acpype_.\n\nTo get help and more information, type:\n\n```bash\n./run_acpype.py -h\n```\n\n##### To Install\n\nAt folder `acpype/`, type:\n\n```bash\n ln -fsv \"$PWD/run_acpype.py\" /usr/local/bin/acpype\n```\n\nThen re-login or start another shell session.\n\nIf via `conda` or `pip`, `acpype` should be in your `$PATH`.\n\n##### To Verify with GMX\n\nGROMACS < v.5.0\n\n```bash\ncd FFF.acpype/\ngrompp -c FFF_GMX.gro -p FFF_GMX.top -f em.mdp -o em.tpr\nmdrun -v -deffnm em\n# And if you have VMD\nvmd em.gro em.trr\n```\n\nGROMACS > v.5.0\n\n```bash\ncd FFF.acpype/\ngmx grompp -c FFF_GMX.gro -p FFF_GMX.top -f em.mdp -o em.tpr\ngmx mdrun -v -deffnm em\n# And if you have VMD\nvmd em.gro em.trr\n```\n\n##### For MD, do\n\nGROMACS < v.5.0\n\n```bash\ngrompp -c em.gro -p FFF_GMX.top -f md.mdp -o md.tpr\nmdrun -v -deffnm md\nvmd md.gro md.trr\n```\n\nGROMACS > v.5.0\n\n```bash\ngmx grompp -c em.gro -p FFF_GMX.top -f md.mdp -o md.tpr\ngmx mdrun -v -deffnm md\nvmd md.gro md.trr\n```\n\n#### To Emulate `amb2gmx.pl`\n\nFor any given _prmtop_ and _inpcrd_ files (outputs from AMBER LEaP), type:\n\n```bash\nacpype -p FFF_AC.prmtop -x FFF_AC.inpcrd\n```\n\nThe output files `FFF_GMX.gro` and `FFF_GMX.top` will be generated inside folder _FFF_GMX.amb2gmx_\n\n#### To Verify with CNS/XPLOR\n\nAt folder _FFF.acpype_, type:\n\n```bash\ncns < FFF_CNS.inp\n```\n\n#### To Verify with NAMD\n\n- see [TutorialNAMD](../../wiki/Tutorial-NAMD)\n",
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JSON
