ChemShell Tools

Introduction

• Restraints
• ESP/RESP charges
• Pointcharge
• Least-Square fit of structures
• Modules, trance, and profile

Restraints

Restraints allow to apply geometry dependent energy terms additional to the energy provided by the theory= keyword. They can be used for umbrella sampling simulations as well as for "constrained" optimisation. The latter is required for calculating reaction profiles.

Restraints can be used in the driver modules energy, gradient, eandg, dynamics, hdlcopt, and dl-find. In these cases, only the keyword restraints= has to be included into the specification of the driver. The other keywords given below are added by the drivers.

Restraints can also be used as a standalone energy/gradient evaluator (invoked by the keyword theory=restraint), representing a simple force field.

Command Line Arguments

Harmonic restraints of the form V=K/2 (x-x₀)² are applied to different types of coordinates x. In each energy evaluation, a list of the types of restraints, their actual value x (in the same units as x₀) and the associate restraint energy V are written to stdout.

# Atomic units:
set ReactionCoordinate 0.3

# atoms to move: 51 37 36
hdlcopt coords=c active_atoms= {51 37 36} \
    theory=restraint : [ list restraints= [ list [ list \
        bonddiff2 51 37 37 36 $ReactionCoordinate 3.0 ] ] ] \
    result=moved.c

ESP Charges

ESP charges of a QM calculation require the potential at a set of points around the molecule. As some programs (mndo, turbomole 5.71) are able to calculate the potential, but do not (correctly) calculate ESP charges, this feature in included in ChemShell.

The set of points can be calculated by get_esp_points. The positions of the points are written into the fragment specified by grid. The QM method should write the potential into the charge-tags of this fragment. Thus, a possible code to generate (R)ESP charges could be as follows.

Command Line Arguments to get_esp_points

Command Line Arguments to fit_esp_charges

Pointcharge

Pointcharge can be used in the program as a qm_theory in hybrid calculations, thus it is in fact an energy+gradient module. It calculates the electrostatic interaction of atomic charges with point charges of the MM atoms (bq charges). The self-energy of the atomic point charges is not included. Forces on the QM atoms are not calculated.

Usage of this module only makes sense if the point charges are obtained from esp charges of a real QM-calculation. Additionally the QM atoms should be frozen.

It is needed to perform FEP calculations, see the manual of the hybrid module.

Command Line Arguments

  open(unit=125,file='charges.bin',form='unformatted')
  write(125) qmat
  do iat=1,qmat
     write(125) r(:,iat),charge(iat)
  end do
  close(125)
  

lsqfit

Command Line Arguments

Argument	Argument type	Mandatory	Default	To specify
coords	Fragment tag	yes	-	Fragment object to be transformed
reference_coords	Fragment tag	yes	-	Reference fragment object
result	Fragment tag	yes	-	Result object
prerotation	file	no	-	Pre-rotation matrix file
correspondence	Tcl List	no	-	Correspondence list for atoms

Description:

A pre-rotation matrix may be optionally supplied, and this is applied to the input structure before the fit is performed. It can be used to fit a structure to its enantiomer.

The corresponce= argument can be used to specify which atoms to be matched, the default is all. It is a list of two-element lists, each pair indicating the corresponding atoms in the first and second fragments, respectively.

e.g.

read_input prerot { 1.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 -1.0 }

lsqfit reference_coords=structure1 coords=structure2 result=res \
prerotation = prerot correspondence = { { 1 1} { 3 2} { 2 3 } }

Modules, trace, and profile

start_module

write_pdb/=============================== Tstep:    0.1 Ttot:    8.2 ==

end_module

parsearg

times

The command times, which takes no arguments, does a simple profiling. It writes a summary of the runtimes used by external programs and by ChemShell modules at the time called. Most useful at the end of ChemShell scripts.