Nucleic Acids

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Distance

DD, DIS, MDIS, MDISG, ODIS, OPOS, OPOS2, ORAD, ORAD2, POS, RAD

Angle

ANG, ANG2, AXANG, AXANG2, DIH, DIH2, PANG, PVANG

Coordination

CNFF, CNGFF, CNSW, CNGSW, CNRF, CNGRF

Shape

ACYL, ASPH, EVEC, PMGTD, PMOGT, PLANE, RGYR, RMSDT, SANIS

Nucleic Acids

NALBPP, NASBPP, NASBPPOLD, NALSTP, NASSTP, NASSTPOLD, NASBO, NAPBO, NABEND

Puckering

PUCK6Q, PUCK6P, PUCK6T, PUCK5Q, PUCK5P

Special

WORMPOS, WORMANG

Energy

POT, EGAP

Algebra

ADD, SUB, MULT, DIV, FSWITCH, RSWITCH

Collective Variables For Nucleic Acids

Type	Description
NASBPP	simple base pair parameters
NASBO	simple base pair opening
NAPBO	primitive base pair opening
NABEND	nucleic acid bending

Simple Base Pair Parameters

All simple base pair parameters (i.e., shear, stretch, stagger, buckle, propeller, opening) fully compatible with 3DNA are available via the NASBPP collective variable. The collective variable NASBO implements only the opening parameter and thus it should be a little bit computationally faster.

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Reference coordinates for nucleobase rings are provided in the following table:

Nucleobase	Ring Atoms	y-axis	File
A	@N9,C8,N7,C5,C6,N1,C2,N3,C4	@C8	A_ring_only.xyz
G	@N9,C8,N7,C5,C6,N1,C2,N3,C4	@C8	G_ring_only.xyz
C	@N1,C6,C5,C4,N3,C2	@C6	C_ring_only.xyz
T	@N1,C6,C5,C4,N3,C2	@C6	T_ring_only.xyz

References

• 3DNA
  • Lu, X.-J.; Olson, W. K. 3DNA: A Versatile, Integrated Software System for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic-Acid Structures. Nature Protocols 2008, 3 (7), 1213–1227. https://doi.org/10.1038/nprot.2008.104.
  • Lu, X.-J.; Olson, W. K. 3DNA: A Software Package for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic Acid Structures. Nucl. Acids Res. 2003, 31 (17), 5108–5121. https://doi.org/10.1093/nar/gkg680.
• Gradients
  • Blanc, E.; Paciorek, W. On Planarity and Similarity Restraints. J. Appl. Crystallogr. 2001, 34, 480–483. https://doi.org/10.1107/S0021889801008470.