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
NALBPP	local base-pair parameters
NASBPP	simple base-pair parameters
NASBPPOLD	simple base-pair parameters (OLD implementation)*
NALSTP	local base-pair step parameters
NASSTP	simple base-pair step parameters
NASSTPOLD	simple base-pair step parameters (OLD implementation)*
NASBO	simple base-pair opening
NAPBO	primitive base-pair opening
NABEND	nucleic acid bending

Base-Pair Parameters

PMFLib offers two variants of the base-pair parameters: local and simple. They differ in the definition of the y-axis and the procedure to calculate six base-pair parameters (i.e., Shear, Stretch, Stagger, Buckle, Propeller, Opening). The simple version is provided by NASBPP, while the local version is provided NASBPP. Both implementations are fully compatible with 3DNA. The collective variable NASBO implements simple Opening only and thus it should be a little bit computationally faster.

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Base-Pair Step Parameters

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.