Torsional space

As the number of conformations increases exponentially with the number of rotatable bonds, for most molecules it is not feasible to take all possible conformations into account. However, a balanced sampling of the conformational space should be ensured if only subsets arc being considered. In order to restrict the number of geometries output, while retaining a maximum of conformational diversity, ROTATE offers the possibility of classifying the remaining conformations, i.c., similar conformations can be combined into classes. The classification is based on the RMS deviation between the conformations, either in Cartesian (RMS y 7if [A]) or torsion space in [ ], The RMS threshold, which decides whether two... 

The molecular structure input requires atom types to be assigned, which are not the same from one force field to the next. The input also includes a list of bonds in the molecule. There is not a module to automatically assign atom types. Most of the modules use a Cartesian coordinate molecular structure, except for a few that work with torsional space. The same keyword file is read by all the executables. A little bit of input is obtained by the program either interactively or from an ASCII file piped to standard input, which makes for a somewhat cryptic input file. This system of common input files and the user choosing which executables to run give TINKER the ability to run very sophisticated simulations while keeping the input required for simple calculations fairly minimal within the limitations mentioned here. 

The OMEGA version 1.8 program [19] was used for this experiment. OMEGA couples a systematic search in torsion space with rules for certain torsions. This approach is computationally efficient, and ideal for this large-scale exercise. 

Keywords Monte Carlo simulations polypeptides polynucleotides concerted rotations multicanonical ensemble torsional space... 

Favrin, G., Irback, A., Sjunnesson, F. Monte Carlo update for chain molecules biased Gaussian steps in torsional space. J. Chem. Phys. 2001, 114, 8154 8. 

Another optimization method, related to the least-squares fitting used in point-based algorithms, is the directed tweak method [31]. This is a torsional space optimizer, in which the rotatable bonds of the ligands are adjusted at search time to produce a conformation which matches the 3D query as closely as possible. As directed tweak involves the use of analytical derivatives, it is very fast and allows for an RMS fit to consider ligand flexibility. 

Metric Matrix, Linearized Embedding, and Torsional Space Methods... 

Although Eq. (4.1) involves an infinite sum, a set of random torsion space vectors 2 having distribution pwo is easily generated by first generating a set of unwrapped vectors 2U having the Cartesian distribution /i°[ 2°, E° 2] [as in Eq. (2.4)] and mapping each 2U onto by... 

Additionally, the torsional minima for the rotatable bonds in DHA are very broad. Results of the biased sampling phase from conformational memories (CM) calculations of AA are consistent with all of these results (Bamett-Norris et al., 1998), as they reveal a relatively broad distribution of populated torsional space about the classic skew angles of -119°(s ) and 119°(s) for the... 

Essentially, the problem of adiabatic leak is mitigated by the presence of constraints, whether in the form of steric hindrance, external forces, or in reduction of dimensionality (for example, simulations in torsion space). In simulations of proposed nanomachines, for example, rigid body dynamics is sometimes applied to components or substructures in order to make the entire nanostructure more rigid. All of this suggests that the prediction of failure modes in some nanomachine designs due strictly to vibrational motion is overly pessimistic. However, this does not by any means minimize concerns such as the difficulty of building desired nanostructures, chemical reactivity. 

Carbon, nitrogen, and oxygen atoms—only sp hybridized—are combined in all possible ways, and a modified chain closure algorithm is used to solve the trigonometric equations in torsional space. Branching is not allowed. Chemical rules are used to eliminate undesirable combinations of atoms such as peroxides. 

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