!EXAMPLE AMBER trpzip 
!for transition state connections with natural internals

This archive contains all you need to perform transition state connection benchmarks for the general natural internal coordinate interpolation method. 

For different methods, change the odata files:
for standard Cartesian interpolation, delete INTINTERP and INTMINPERM lines
for CHARMM internal coordinate interpolation for sidechains only,delete INTINTERP and INTMINPERM lines, and add AMBERSTEP\\ AMBERIC\\ AMBICDNEB\\ (\\indicates linebreak)
for  CHARMM internal coordinate interpolation for sidechains and backbone, delete INTINTERP and INTMINPERM lines, and add AMBERSTEP\\ AMBERIC BACKBONE\\ AMBICDNEB (\\indicates linebreak)
for natural internal coordinate interpolation with the same number of (not equispaced) image points as required in DNEB, add INTERPSIMPLE
for choosing the interpolation coordinate system (natural internals or Cartesians) according to energy of the images add INTERPCHOICE
for not aligning according to a internal coordinate metric, delete INTMINPERM
for aligning prochiral methylene carbons according to a distance metric (not recommended!), delete NOPERMPROCHIRAL
for using internal distance in the DIJKSTRA search, add INTDISTANCE to DIJKSTRA EXP at the end (recommended)

* odata - OPTIM input file (all lines beginning with COMMENT may be safely removed)
* coords.inpcrd - AMBER coordinate input file for trpzip
* coords.prmtop - AMBER topology file for the ff03 forcefield for trpzip
* min.in - AMBER forcefield minimisation input file
* output/ - directory containing the expected output
* README - this file!
