Phi-Psi Map Lesson, Input File

When you execute most of the commands in the Discover_3 module, you are actually building up a command input file, which is written to disk when the D_Run/Run command is executed. The command input file consists of a BTCL script that controls the Discover run.

This example file contains links to the complete descriptions of the BTCL commands. The BTCL language. Added comments that were not part of the original file are in italics.

Default values that are not specified in the command input file are shown in the output file.

#BIOSYM btcl 3
#
#  Input File For Discover Generated By Insight Version 95.0Beta
#  Date:	   Wed Jun 14 11:28:40 1995
#  User Name: marj  
#  Host Name: iris90  
#  Host Type: iris
#
#  System Name: PP 
#
#Stage Name: 1  begin
  begin
#

A subset of the default forcefield is specified:

#Stage Name: 2  nonbonds
  forcefield nonbond \
    -separate_coulomb \
    vdw \
      summation_method = no_cutoff \
    coulomb \
      -distance_dependent_dielectric
#

The variable for counting loops is initialized:

#Stage Name: 3  comment
$count = 0

The loop over the phi torsion:

#Stage Name: 4  loop
for {$phi = -180} {$phi <= 180} {$phi = $phi + 30} {
#
#Stage Name: ..5  geometry
  molGeom  set \
    torsion  $phi \
    "PP:1:C1"  "PP:1:C2"  "PP:1:C3"  "PP:1:C4" 
#
#Stage Name: ..6  restraint
    restraint create "5__restraint" torsion "PP:1:C1" "PP:1:C2" "PP:1:C3" "PP:1:C4"
    restraint function "5__restraint" cosine "1000.0" "1"
    restraint target "5__restraint"  "$phi"  
#

The loop over the psi torsion:

#Stage Name: ..7  loop
  for {$psi = -180} {$psi <= 180} {$psi = $psi + 30} {
#
#Stage Name: ....8  command
      $count = $count + 1
#
#Stage Name: ....9  geometry
    molGeom  set \
      torsion  $psi \
      "PP:1:C2"  "PP:1:C3"  "PP:1:C4"  "PP:1:C5" 
#
#Stage Name: ....10  restraint
      restraint create "8__restraint" torsion "PP:1:C2" "PP:1:C3" "PP:1:C4" "PP:1:C5"
      restraint function "8__restraint" cosine "1000.0" "1"
      restraint target "8__restraint"  "$psi"  
#
#Stage Name: ....11  minimize
    minimize \
      iteration_limit = 300 movement_limit = 0.200 \
      sd \
        convergence = 1000.0 line_search_precision = 0.100 \
      cg \
        convergence = 10.0 method = polak \
        line_search_precision = 0.100 \
      newton \
        convergence = 0.001 method = bfgs \
        line_search_precision = 0.900 max_atoms = 200 \
      final_convergence = 0.001
    #
    writeFile coordinate filename = .cor 
#
#Stage Name: ..12  file control
    writeFile archive frame = $count
#
#Stage Name: ..13  end
  }
#
#Stage Name: 14  end
}

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Phi-Psi Map Lesson, Introduction Phi-Psi Map Lesson, Lesson