#!/bin/sh

# In this example we use the amber forcefield that cannot guess atom types

# First we "calculate" the types

# We do this by specifying them as atom attributes (ForceField.Type)

export AMS_JOBNAME=CalculateTypes

rm -rf $AMS_JOBNAME.results

$AMSBIN/ams << eor
Task GeometryOptimization

Properties Charges=yes

System
   Atoms
     C       1.94807   3.58290  -0.58162       ForceField.Charge=0.0       ForceField.Type=CT
     H       1.69949   4.49893  -1.05273       ForceField.Charge=0.0       ForceField.Type=HC
     H       2.99455   3.17964  -0.86304       ForceField.Charge=0.0       ForceField.Type=HC
     C       0.94659   2.40054  -0.92364       ForceField.Charge=0.0       ForceField.Type=CT
     C       1.94191   3.61595   1.09448       ForceField.Charge=0.0       ForceField.Type=CT
     N      -1.74397  -3.46417   0.31178       ForceField.Charge=-0.9530   ForceField.Type=N2
     C      -1.00720  -2.20758   0.33536       ForceField.Charge=0.8185    ForceField.Type=CA
     C      -1.66928  -1.00652   0.31001       ForceField.Charge=-0.5215   ForceField.Type=CM
     C      -0.92847   0.25653   0.34895       ForceField.Charge=0.0053    ForceField.Type=CM
     N       0.43971   0.26735   0.38232       ForceField.Charge=-0.0484   ForceField.Type=N*
     N       0.36409  -2.20477   0.28992       ForceField.Charge=-0.7584   ForceField.Type=NC
     C       1.09714  -0.95413   0.22469       ForceField.Charge=0.7538    ForceField.Type=C
     H      -2.89781  -3.50815   0.31746       ForceField.Charge=0.4234    ForceField.Type=H
     H      -1.21484  -4.49217   0.31721       ForceField.Charge=0.4234    ForceField.Type=H
     H      -2.80940  -0.93497   0.30550       ForceField.Charge=0.1928    ForceField.Type=HA
     H      -1.55324   1.21497   0.33885       ForceField.Charge=0.1958    ForceField.Type=H4
     C       1.23309   1.44017   0.30994       ForceField.Charge=0.0066    ForceField.Type=CT
     O       2.58277  -1.01636   0.23914       ForceField.Charge=-0.6252   ForceField.Type=O
     H       2.37276   1.25557   0.29984       ForceField.Charge=0.2902    ForceField.Type=H2
     O       1.02358   2.43085   1.50880       ForceField.Charge=-0.2033   ForceField.Type=OS
     H       1.17136   1.95097  -1.87367       ForceField.Charge=0.0       ForceField.Type=HC
     H      -0.10600   2.77333  -0.80348       ForceField.Charge=0.0       ForceField.Type=HC
     H       1.62170   4.54039   1.51392       ForceField.Charge=0.0       ForceField.Type=H1
     H       2.99608   3.28749   1.41345       ForceField.Charge=0.0       ForceField.Type=H1
   End
End

Engine ForceField
   Type Amber95
EndEngine

eor


# Now we load the types from the previous result

# The result should be identical to the first calculation

export AMS_JOBNAME=LoadTypes

rm -rf $AMS_JOBNAME.results

$AMSBIN/ams << eor
Task GeometryOptimization

System
   Atoms
     C       1.94807   3.58290  -0.58162
     H       1.69949   4.49893  -1.05273
     H       2.99455   3.17964  -0.86304
     C       0.94659   2.40054  -0.92364
     C       1.94191   3.61595   1.09448
     N      -1.74397  -3.46417   0.31178
     C      -1.00720  -2.20758   0.33536
     C      -1.66928  -1.00652   0.31001
     C      -0.92847   0.25653   0.34895
     N       0.43971   0.26735   0.38232
     N       0.36409  -2.20477   0.28992
     C       1.09714  -0.95413   0.22469
     H      -2.89781  -3.50815   0.31746
     H      -1.21484  -4.49217   0.31721
     H      -2.80940  -0.93497   0.30550
     H      -1.55324   1.21497   0.33885
     C       1.23309   1.44017   0.30994
     O       2.58277  -1.01636   0.23914
     H       2.37276   1.25557   0.29984
     O       1.02358   2.43085   1.50880
     H       1.17136   1.95097  -1.87367
     H      -0.10600   2.77333  -0.80348
     H       1.62170   4.54039   1.51392
     H       2.99608   3.28749   1.41345
   End
   LoadForceFieldCharges    file=CalculateTypes.results
   LoadForceFieldAtomTypes  file=CalculateTypes.results
End

Engine ForceField
   Type Amber95
   Verbosity Verbose

EndEngine

eor