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 or 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.

This code is released under GNU General Public License V3.

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

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 http://www.biomedcentral.com/1756-0500/5/367

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 Wilter Sousa da Silva, D.Sc. Bioinformatician, UniProt, EMBL-EBI Hinxton, Cambridge CB10 1SD, UK. http://www.ebi.ac.uk/~awilter

alanwilter at gmail dot com

How To Use ACPYPE

Introduction

We now have an up to date webservice at http://bio2byte.be/acpype/ (but it does not have the amb2gmx funcionality).

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 several ways of obtaining acpype:

1) Via CONDA:

  conda install -c conda-forge acpype

or, if you want to be sure to get the latest (sometimes conda-forge channel is still lagging behind)

  conda install -c acpype acpype

2) Via PyPI:

  pip install git+https://github.com/alanwilter/acpype.git

note that pip install acpype, unfortunately, is not picking the original one.

3) By downloading it via git:

  git clone https://github.com/alanwilter/acpype.git

4) Via Docker:

If you have Docker installed, you can run Acpype with the following shell command:

On Linux / MacOS:

docker run --rm -v ${PWD}:/results -w /results -u $(id -u ${USER}):$(id -g ${USER}) lpkagami/acpype:latest -i FFF.pdb

On Windows: Using Command Prompt:

docker run --rm -v %cd%:/results -w /results -u root lpkagami/acpype:latest -i FFF.pdb

Using PowerShell:

docker run --rm -v ${PWD}:/results -w /results -u root lpkagami/acpype:latest -i FFF.pdb

NB: Installing via conda gives you AmberTools17 and OpenBabel2.4, while via pip/git you get AmberTools19 and OpenBabel3 (which lacks obchiral, but this is not critical). Our AmberTools19 comes with binary charmmgen from AmberTools17 in order to generate CHARMM topologies.

To Test, if doing via git

At folder acpype/test, type:

../acpype_lib/acpype.py -i FFF.pdb

It’ll create a folder called FFF.acpype, and inside it one may find topology files for GROMACS and CNS/XPLOR.

To get help and more information, type:

../acpype.py -h
To Install

At folder acpype, type:

  ln -s $PWD/acpype.py /usr/local/bin/acpype

And re-login or start another shell session.

If via conda or pip, acpype should show 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
With openmpi, for a dual core

GROMACS < v.5.0

grompp -c FFF_GMX.gro -p FFF_GMX.top -f em.mdp -o em.tpr
om-mpirun -n 2 mdrun_mpi -v -deffnm em
grompp -c em.gro -p FFF_GMX.top -f md.mdp -o md.tpr
om-mpirun -n 2 mdrun_mpi -v -deffnm md
vmd md.gro md.trr

GROMACS > v.5.0

gmx grompp -c FFF_GMX.gro -p FFF_GMX.top -f em.mdp -o em.tpr
gmx mdrun -ntmpi 2 -v -deffnm em

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 at the same folder of the input files.

To Verify with CNS/XPLOR

At folder FFF.acpype, type:

cns < FFF_CNS.inp

To Verify with NAMD

  • see [TutorialNAMD]