!EXAMPLE CHARMM GNNQQNY
!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 CHINTERPOLATE BC SI DNEB
for  CHARMM internal coordinate interpolation for sidechains and backbone, delete INTINTERP and INTMINPERM lines, and add CHINTERPOLATE BI SI DNEB
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


* odata - OPTIM input file (all lines beginning with COMMENT may be safely removed)
* input.crd - CHARMM coordinate input file for starting structure for GNNQQNY
* finish - CHARMM coordinate input file for finishing structure GNNQQNY
* perm.allow - file containing possible permutational isomers
* output/ - directory containing the expected output
* README - this file!
