Current Problems in Computer Simulation of Variability …
249
Fig. 7 Initial structure extracted from a DNA fragment with NDB id 2MAV (upper row) and
DFT/PW91-ulg optimized structure (lower row) of dApdT:dApdT. Base pair closer to the observer
has H-bonds marked with black dotted line; left dDMP is in 110 conformation family, right dDMP
is in BI conformation family
have shortened atom-atom contacts that diminishes the quality of these models. Similar results have been obtained for a few other cdDMPs containing one or two dDMPs
belonging to non-canonical B-like conformation families.
Experimentation with different DFT functionals on computation of these noncanonical cdDMPs led us to dispersion corrected functional PW91-ulg, which does
not produce short atom-atom contacts between the stacked bases. Application of this
functional to optimization of several cdDMPs consisting of two dDMPs belonging
to different B-like conformation families produces the structures that have conformational features resembling those obtained with the use of M05-2X functional but
without shortened contacts. Tables 2 and 3 demonstrate the similarity in torsion
249
Fig. 7 Initial structure extracted from a DNA fragment with NDB id 2MAV (upper row) and
DFT/PW91-ulg optimized structure (lower row) of dApdT:dApdT. Base pair closer to the observer
has H-bonds marked with black dotted line; left dDMP is in 110 conformation family, right dDMP
is in BI conformation family
have shortened atom-atom contacts that diminishes the quality of these models. Similar results have been obtained for a few other cdDMPs containing one or two dDMPs
belonging to non-canonical B-like conformation families.
Experimentation with different DFT functionals on computation of these noncanonical cdDMPs led us to dispersion corrected functional PW91-ulg, which does
not produce short atom-atom contacts between the stacked bases. Application of this
functional to optimization of several cdDMPs consisting of two dDMPs belonging
to different B-like conformation families produces the structures that have conformational features resembling those obtained with the use of M05-2X functional but
without shortened contacts. Tables 2 and 3 demonstrate the similarity in torsion