DBT can be used to build polymer (linear or hyperbranched) in AMBER depending upon multiplicity of joining residues (For more details please see tutorial and refer article: J. Comput. Chem. 2012, 33, 1997-2011). Thus DBT is a graphical user interface (GUI) written in PERL-Tk, which generates a set of commands (xleap/tleap) to be used further by AMBER. DBT has been integrated with AMBER10. DBT sequences and calculates the number of residues required for building dendrimer (or polymer), which further depends on core multiplicity and generation of dendrimer.
Please refer:
System requirements: Linux, PERL-Tk, AMBER10, AMBERTOOL1.2 (You can try on other versions of AMBER (11 or 12), but DBT was used and tested with the mentioned versions)
Two-phase thermodynamic (2PT) model is used for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component.
Please refer:
System requirements: Linux, PERL-Tk, AMBER10, AMBERTOOL1.2 (You can try on other versions of AMBER (11 or 12), but DBT was used and tested with the mentioned versions)