COMMENT !------------------------------------------------------------------------------!
COMMENT ! EXAMPLE A9OPTIM INPUT - single minimum normal mode analysis of met-enkephalin!
COMMENT ! Tested for r15589 of A9OPTIM (01/05/09)                                      !
COMMENT !------------------------------------------------------------------------------!

COMMENT <KEYWORD SUMMARY>
COMMENT DEBUG : DEBUG included to give you more output to look at
COMMENT BFGSMIN 1D-6 : calls for an LBFGS minimisation until the root-mean-square gradient converges to 10^(-6)
COMMENT STEPS 2000 : Do up to 2000 steps of optimisation
COMMENT DUMPVECTOR ALLVECTORS MWVECTORS : Dump all (ALLVECTORS) mass-weighted (MWVECTORS) Hessian eigenvectors (the normal modes) to 
COMMENT                                   vector.dump with frequencies in cm-1. Also dump PDBs describing the per atoms and per residue 
COMMENT                                   displacement resulting from the action of these vectors 
COMMENT KTWN 212.67 : Set kT in cm^(-1) to 212.67 corresponding to the temperature in the upper respiratory tract of humans. This is used 
COMMENT               to Boltzmann weight the atomic and residue displacements caused by thermally accessible normal modes (defined by 
COMMENT               frequency < kT)
COMMENT DUMPMODE 1 2 10 : Dump modes 1, 2 and 10 to individual PDB files for later visualisation
COMMENT DUMPSTRUCTURES : Specifies that final structures should be dumped for the AMBER 9 runs into pdb, AMBER restart and xyz formats
COMMENT NAB coords.inpcrd inpcrd : Specifies a calculation with the interfaced version of the Nucleic Acid Builder program package. From 
COMMENT                            this package the Amber force fields are being used only. This is required to call analytical second 
COMMENT                            derivative evaluations. The AMBER input file and file type is also specified here.

REOPTIMISEENDPOINTS
RIGIDINIT

DEBUG
comment STEPS 1000
comment DUMPVECTOR ALLVECTORS MWVECTORS
comment KTWN 212.67
comment DUMPMODE 1 2 10 
DUMPSTRUCTURES

DUMPDATA
ENDHESS
comment ENDNUMHESS
MAXERISE 1.0D-4 1.0D0
BFGSMIN 1.0D-3
BFGSSTEPS 20000
MAXBFGS 0.2
NAB coords.inpcrd inpcrd 
comment AMBER9 coords.inpcrd inpcrd 
comment POINTS
