- Parameter/topology file specification (
prmtop) - Coordinate/restart file specification (
inpcrd, restrt) - Trajectory (velocity or coordinate) file specification (
mdcrd, mdvel) - Binary (NetCDF) trajectory (velocity or coordinate) file specification (
mdcrd, mdvel) - Force field parameter file specifications:
- Main parameter set (
parm*.dat) - Parameter modification file (
frcmod)
- Main parameter set (
- OFF Library files, useful for understanding Amber residue library files using the Object File Format (OFF) specification.
- Prep input files, useful for understanding the topology database files, and Antechamber output files.
``PARM' parameter/topology file specification
The following section provides a good overview of the general topology fileformat. A more complete prmtop specification, complete withchamber-style sections and expanded explanations of some sections andhow they are used to calculate forces in Amber programs, is available inPDF-form by clicking here. (This document is takenfrom the appendix of Jason Swails’ doctoral dissertation.) This file isgenerated by the LEaP programs, either sleap or tleap/xleap.
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NOTE: the atom numbers in the following arrays that describe bonds,angles, and dihedrals are coordinate array indexes for runtime speed. The trueatom number equals the absolute value of the number divided by three, plus one.In the case of the dihedrals, if the fourth atom is negative, this implies thatthe dihedral is an improper. If the third atom is negative, this implies thatthe end group interations are to be ignored. End group interactions areignored, for example, in dihedrals of various ring systems (to prevent doublecounting of 1-4 interactions) and in multiterm dihedrals.
The following are only present if IFBOX .gt. 0
The following are only present if IFCAP .gt. 0
The following is only present if IFPERT .gt. 0 Note thatthe initial state, or equivalently the prep/link/edit state, isrepresented by lambda=1 and the perturbed state, or final statespecified in parm, is the lambda=0 state. This information is only used forGIBBS and is unused in either SANDER or PMEMD.
The following is only present if IPOL .eq. 1
The following is only present ifIPOL 1 .and. IFPERT 1
AMBER coordinate/restart file specification
The 'coord' version of this file is generated by the PARM orLEaP programs. The 'restrt' version is the result of energyminimization or molecular dynamics in SANDER orGIBBS and may contain velocity and periodic box information.
IF dynamics
IF constant pressure (in 4.1, also constant volume)
Note: in AMBER 4.1 if the EWALD option is turned on, the box angles willalso be written out in the same format.
AMBER trajectory (coordinate or velocity) file specification
This file is optionally written during dynamics inSANDER orGIBBS.The following snapshot is written every NTWX steps in thetrajectory (specified in the control input file):
IF constant pressure (in 4.1, also constant volume), for eachsnapshot:
AMBER Trajectory NetCDF Convention
Beginning with AMBER 9, a binary file format for trajectory data based onNetCDF issupported by sander, pmemd and ptraj. This format is supported byVMD beginning with version1.8.4.
How To Read Md Files
The AMBER Trajectory NetCDF Convention,describes the layout of dimensions, variables and attributes within the file. It is also available as a PDF.
Opening Md Files
Force field parameter file specification
Markdown
Force field parameter modification file specification