The source code developed in this thesis to carry out the molecular optimizations (TSSEARCH) has been
implemented in ROAR 2.0 [235] and CHARMM [53] c28b2.
The version implemented in ROAR is called from the main program (sander subroutine)
and it can be downloaded from the web
http://www.qf.uab.es/prat/prog/ts
The version interfaced with CHARMM package is called from the minimization module (minimize.src) and it will be also available along with a short documentation file.
The general scheme of TSSEARCH code is outlined in the scheme B.1 and the name of the subroutines are intended to be autoexplicative. It requires as input the geometry in Cartesian coordinates and the labels that indicate the partition of the system in core and environment zones. As the program proceeds it requires the energy and the gradient from the external program. The subroutine energy_qmmm is the interface between TSSEARCH and external energy and gradient code and it must be modified depending on the requirements of the external program.
In some cases the original energy subroutines had to be modified, for instance in the ESP/MM or QM(1SCF)/MM approximations. Since either the original or modified subroutines cannot be distributed please contact the author of this thesis for any question.
Finally you may find also on the web the source code that calculates the potential of mean
force from the distribution function ouput by CHARMM used in chapter 4.
http://www.qf.uab.es/prat/prog/pmf