March 19, 2016 at the Amber developer meeting at UCSD

16 Pages·2016·1.85 MB·English

ParmEd
Jason Swails, Amber Meeting 2016
Rafal Wiewiora, John Chodera
Outline
What is it?
Who uses it, and for what?
What’s new?
What is it?
Standalone programs API
Easily instantiate and
bash$ parmed
/^^^/ /]
/ ] / ] m a n i p u l a t e f u l l M M
_______/ ]___ / ]
/ \_____/ /
descriptions of chemical
_/ [@] \ \ \
/.. | | ]
systems.
VVVvvv\ | | _/\ ]
P A R M E D | / \ ]
AAA^^^^^ / \]
\_________\ \_____/
\ \
Support wide range of
\____\
force fields and potential
ParmEd: a Parameter file Editor
energy functions.
Reading input from STDIN...
> help
Documented commands (type help <topic>):
Read and write dozens
========================================
EOF changeRadii minimize quit
HMassRepartition checkValidity netCharge scale o f file types from many
OpenMM defineSolvent outCIF scee
add12_6_4 deleteBond outPDB scnb
programs
addAtomicNumber deleteDihedral outparm setAngle
[snip]
>
Dimensional Analysis
Dimensional Analysis
Overhauled API
prmtop
PSF file
Parsers/
PDB File
(and parameters)
Writers
PDBFile CharmmPsfFile AmberParm
PDBx/
CIFFile
mmCIF
mol2 Mol2File Structure base class
System +
…
GromacsTopFile
Topology
OMM System and Topology Gromacs top/itp
Supported File Formats
Mol2/Mol3
Amber, chamber, and
AMOEBA-style prmtops
CHARMM PSF
Amber restart/mdcrd
CHARMM RTF, PRM, and
STR files
Amber NetCDF restart
and trajectory
CHARMM coordinate
and restart files
Amber parameter/frcmod/
OFF/leaprc files
NAMD binary coordinate
and velocity files
PDB (with metadata)
GROMACS topology/gro
PDBx/mmCIF (with
metadata)
Many others
Simple Interface
Automatic file-type detection upon read
Simple Interface
Automatic file-type detection upon write
Details of the conversion are automatically handled
Who uses it, and for what?
sander Python API
Phenix
CHARMM-GUI
InterMol*
Numerous Amber
utilities Force Field
converters
OpenMolTools