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        "author": "SOUSA DA SILVA, A. W.; VRANKEN, W. F.; LAUE, E. D. ACPYPE - AnteChamber",
        "author_email": "acpype@acpype.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 2 - Pre-Alpha",
            "Intended Audience :: Developers",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.6",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5"
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        "description": "-------\nACPYPE\n-------\n\nA tool based in Python to use Antechamber to generate topologies for chemical\ncompounds and to interface with others python applications like CCPN or ARIA.\n\nacpype is pronounced as \"ace + pipe\"\n\nTopologies files to be generated so far: CNS/XPLOR, GROMACS, CHARMM and AMBER.\n\nNB: 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:\nhttp://ffamber.cnsm.csulb.edu/) as well as to XPLOR/CNS (see xplor-nih:\nhttp://ambermd.org/xplor-nih.html) and CHARMM.\n\nThis code is released under GNU General Public License V3.\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:\n  http://www.yasara.org/autosmiles.htm (Elmar Krieger)\n\n* topolbuild (Bruce Ray)\n\n* xplo2d (G.J. Kleywegt)\n\nFor Antechamber, please cite:\n1.  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.\n2.  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.\n\nIf you use this code, I am glad if you cite:\n\nSOUSA DA SILVA, A. W.; VRANKEN, W. F.; LAUE, E. D. ACPYPE - AnteChamber\nPython Parser Interface. Manuscript to be submitted.\n\nAlan Wilter S. da Silva, D.Sc. - CCPN Research Associate\nDepartment of Biochemistry, University of Cambridge.\n80 Tennis Court Road, Cambridge CB2 1GA, UK.\n>>http://www.bio.cam.ac.uk/~awd28<<\n\nalanwilter _at_ gmail _dot_ com\n\n----------------------\nHow To Use ACPYPE\n----------------------\n\n----------------------\nIntroduction\n----------------------\n\nTo run *acpype* with its all functionalities, you need *ANTECHAMBER* from package\n[http://amber.scripps.edu/#AmberTools AmberTools] and\n[http://openbabel.org/wiki/Main_Page Open Babel] 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 *[http://www.python.org Python]*.\n\nAt the moment, *acpype* is only available for download via *svn*:\n\n  * `svn checkout http://acpype.googlecode.com/svn/trunk/ acpype`\n\nYet, if some reason you cannot use *svn*, one still can get *acpype* with:\n\n  * `wget http://acpype.googlecode.com/svn/trunk/acpype.py`\n\nBut be aware that one may run in extra troubles and I am not willing to support\nthis way.\n\n----------------------\nTo Test\n----------------------\n\nAt folder *acpype/test*, type:\n\n  * `../acpype.py -i FFF.pdb`\n\nIt'll create a folder called *FFF.acpype*, and inside it one may find topology\nfiles for GROMACS and CNS/XPLOR.\n\nTo get help and more information, type:\n\n  * `../acpype.py -h`\n\n----------------------\nTo Install\n----------------------\n\nAt folder *acpype*, type:\n\n  * `ln -s $PWD/acpype.py /usr/local/bin/acpype`\n\nAnd re-login or start another shell session.\n\n----------------------\nTo Verify with GMX\n----------------------\n\n{{{\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# For MD, do:\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# with openmpi, for a dual core\ngrompp -c FFF_GMX.gro -p FFF_GMX.top -f em.mdp -o em.tpr\nom-mpirun -n 2 mdrun_mpi -v -deffnm em\ngrompp -c em.gro -p FFF_GMX.top -f md.mdp -o md.tpr\nom-mpirun -n 2 mdrun_mpi -v -deffnm md\nvmd md.gro md.trr\n}}}\n\nTo Emulate _[http://ffamber.cnsm.csulb.edu/tools.html amb2gmx.pl]_\n\nFor any given *prmtop* and *inpcrd* files (outputs from AMBER LEaP), type:\n\n  * ` acpype -p FFF_AC.prmtop -x FFF_AC.inpcrd`\n\nThe output files `FFF_GMX.gro` and `FFF_GMX.top` will be generated at the same\nfolder of the input files.\n\n-------------------------\nTo Verify with CNS/XPLOR\n-------------------------\n\nAt folder *FFF.acpype*, type:\n\n  * `cns < FFF_CNS.inp`\n\n----------------------\nTo Verify with NAMD\n----------------------\n\n  * see [TutorialNAMD]\n\n\n=======\nHistory\n=======\n\n0.1.0 (2017-01-04)\n------------------\n\n* First release on PyPI.\n\n\n",
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