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Project description

ACPYPE

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 Antechamber, please cite: 1. Wang, J., Wang, W., Kollman P. A.; Case, D. A. “Automatic atom type and bond type perception in molecular mechanical calculations”. Journal of Molecular Graphics and Modelling , 25, 2006, 247260. 2. Wang, J., Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. “Development and testing of a general AMBER force field”. Journal of Computational Chemistry, 25, 2004, 1157-1174.

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

SOUSA DA SILVA, A. W.; VRANKEN, W. F.; LAUE, E. D. ACPYPE - AnteChamber Python Parser Interface. Manuscript to be submitted.

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate Department of Biochemistry, University of Cambridge. 80 Tennis Court Road, Cambridge CB2 1GA, UK. >>http://www.bio.cam.ac.uk/~awd28<<

alanwilter _at_ gmail _dot_ com

How To Use ACPYPE

Introduction

To run acpype with its all functionalities, you need ANTECHAMBER from package [http://amber.scripps.edu/#AmberTools AmberTools] and [http://openbabel.org/wiki/Main_Page 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 [http://www.python.org Python].

At the moment, acpype is only available for download via svn:

  • svn checkout http://acpype.googlecode.com/svn/trunk/ acpype

Yet, if some reason you cannot use svn, one still can get acpype with:

  • wget http://acpype.googlecode.com/svn/trunk/acpype.py

But be aware that one may run in extra troubles and I am not willing to support this way.

To Test

At folder acpype/test, type:

  • ../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.

To Verify with GMX

{{{ 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

# For MD, do: grompp -c em.gro -p FFF_GMX.top -f md.mdp -o md.tpr mdrun -v -deffnm md vmd md.gro md.trr

# with openmpi, for a dual core 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 }}}

To Emulate _[http://ffamber.cnsm.csulb.edu/tools.html 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]

History

0.1.0 (2017-01-04)

  • First release on PyPI.

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