Understanding & Creating BTCL Scripts, Section 3, Command Input File

Note: This file contains hypertext links and html tags and is therefore not directly useful as a command input file for a Discover run. You need to use the seg1.inp file that is found in the $BIOSYM/tutorial/discover/BTCL directory for the actual 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 appear in the output file.

#BIOSYM btcl 3

set PROJECT butane

begin

# Output distance between C1 and C2 and system energy
molGeom get distance d12 "*:1:C1" "*:1:C2"
set ener [energy]
echo d12 = [object d12]
echo energy = $ener
lappend energies $ener
lappend dists [object d12]

# Alter distance between C1 and C2 and output
# new distance and system energy
molGeom set distance relative 0.2 "*:1:C1" "*:1:C2"
molGeom get distance d12 "*:1:C1" "*:1:C2"
set ener [energy]
echo d12 = [object d12]
echo energy = $ener
lappend energies $ener
lappend dists [object d12]

Minimize the conformation:

minimize \
  iteration_limit = 10 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

# Output distance and system energy after minimization
molGeom get distance d12 "*:1:C1" "*:1:C2"
set ener [energy]
echo d12 = [object d12]
echo energy = $ener
lappend energies $ener
lappend dists [object d12]

# Apply a distance restraint between C1 and C2
restraint create rstr distance *:1:C1 *:1:C2
restraint function rstr quadratic 100.0 500.0
restraint target rstr relative 0.2

Minimize again:

minimize \
  iteration_limit = 10 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

# Output distance and system energy after minimization
# with restraint
molGeom get distance d12 "*:1:C1" "*:1:C2"
set ener [energy]
echo d12 = [object d12]
echo energy = $ener
lappend energies $ener
lappend dists [object d12]

Final output:

echo number of data points: [llength $energies]
echo energies: $energies
echo dists: $dists

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BTCL - Tutorial Access.

Lesson on understanding & creating BTCL scripts, Introduction Lesson on understanding & creating BTCL scripts, Section 3