Science Blog of Dr. Yuan分享 This blog is mainly on Molecular molecular modelling and simulations


ParmEd, a cross-program parameter and topology file editor

已有 5156 次阅读 2017-10-3 02:33 |个人分类:科研笔记|系统分类:论文交流


ParmEd is a package designed to facilitate creating and easily manipulatingmolecular systems that are fully described by a common classical force field.Supported force fields include Amber, CHARMM, AMOEBA, and several others thatshare a similar functional form (e.g., GROMOS).

ParmEd is capable of reading and writing to a wide array of different fileformats, like the Amber topology and coordinate files, CHARMM PSF, parameter,topology, and coordinate files, Tinker parameter, topology, and coordinatefiles, and many others. The expressive central data structure (the Structureclass) makes it easy to quickly and safely manipulate a chemical system, itsunderlying topology, and force field parameters describing its potential energyfunction.

There are two parts of ParmEd---a documented API that you can incorporate intoyour own Python scripts and programs, and a GUI/CLI pair of programs thatprovide a means to quickly perform various modifications to chemical systems forrapid prototyping.

The API also provides bindings to the OpenMMlibrary, permitting you to carry out full molecular dynamics investigationsusing ParmEd on high-performant hardware, like AMD and NVidia GPUs.

Installing ParmEd

To install ParmEd, either clone this git repository or download the latestrelease and unpack the resultingtarball. This should create a new ParmEd source code directory. Change to thatdirectory and build ParmEd with the command

python install

Note, if you are using the system Python, you may need to either run the abovecommand as root (e.g., by using sudo) or add the --user flag to installit to your home directory. I would suggest the latter choice.

AMBER user can overwrite installed version by

python install --prefix=$AMBERHOME


import parmed as pmd

# convert GROMACS topology to AMBER format
gmx_top = pmd.load_file('', xyz='pmaawaterFE20mer2.gro')'', format='amber')'pmaa.crd', format='rst7')

# convert AMBER topology to GROMACS, CHARMM formats
amber = pmd.load_file('prmtop', 'inpcrd')
# Save a GROMACS topology and GRO file'')'gromacs.gro')

# Save a CHARMM PSF and crd file'charmm.psf')'charmm.crd')

# convert mol2 to pdb file
mol2_parm = pmd.load_file('my.mol2')'my.pdb')

# and many more

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