= 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:
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.
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
vmd em.gro em.trr
grompp -c em.gro -p FFF_GMX.top -f md.mdp -o md.tpr mdrun -v -deffnm md vmd md.gro md.trr
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 ==