AMBER

USEFUL LINKS

AMBER WIKI
AMBER TUTORIALS
Rizzo Lab AMBER Tutorials

HANDY INPUTS for AMBER

Trajectory post-processing

  • IMIN5

USAGE: $SANDER -O -i imin5.in -o imin5_gb.out -p prmtop -c inpcrd -y mdcrd

imin5.in:

Trajectory post-processing
 &cntrl
   ntx=1, ntpr=1, ntwx=1,
   imin=5,maxcyc=1,ntb=0,
   cut=999.0,ioutfm=1,igb=5,
/
  • PTRAJ

USAGE: $AMBERHOME/exe/ptraj prmtop < ptraj.in > ptraj.out
ptraj.in:

trajin test.mdcrd 1 100 1
trajout new.mdcrd crd
trajout new_netcdf.netcdf netcdf
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