shekfeh / acpype

OFFICIAL: AnteChamber PYthon Parser interfacE

ACPYPE

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) as well as to XPLOR/CNS (see xplor-nih) and CHARMM.

This code is released under GNU General Public Licence V3.

See online documentation 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 (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

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

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

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

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

Alan Silva, DSc

alanwilter at gmail dot com

How To Use ACPYPE

Introduction

We now have an up-to-date web service at Bio2Byte (but it does not have the amb2gmx functionality).

To run acpype, locally, with its all functionalities, you need ANTECHAMBER from package AmberTools and Open Babel 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.

There are several ways of obtaining acpype:

1. Via CONDA:

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

   conda install -c conda-forge acpype

2. Via PyPI:

   If you're using Linux with Intel processors then

   pip install acpype

   is enough and you should have a complete solution. Oterwise ...

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

   # 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)

   # 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:

   (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:

   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:

   setx /M path "%path%;%cd%"

   Commands:

   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:

./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 notation:

./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:

./run_acpype.py -h

To Install

At folder acpype/, type:

  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

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

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

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

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:

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:

cns < FFF_CNS.inp

To Verify with NAMD

• see TutorialNAMD