Nucleic Acids: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 31: | Line 31: | ||
Reference coordinates for nucleobase rings are provided in the following table: | Reference coordinates for nucleobase rings are provided in the following table: | ||
{| | {| | ||
| style="width: 5em;" | Nucleobase | | style="width: 5em;" | '''Nucleobase''' | ||
| | | '''Ring Atoms''' | ||
| '' | | '''y-axis''' | ||
| '''File''' | |||
|- | |- | ||
| A | | A | ||
| | | @N9,C8,N7,C5,C6,N1,C2,N3,C4 | ||
| @C8 | |||
| | | | ||
|- | |- | ||
| G | | G | ||
| | | @N9,C8,N7,C5,C6,N1,C2,N3,C4 | ||
| @C8 | |||
| | | | ||
|- | |- | ||
| C | | C | ||
| | | @N1,C6,C5,C4,N3,C2 | ||
| @C6 | |||
| | | | ||
|- | |- | ||
| T | | T | ||
| | | @N1,C6,C5,C4,N3,C2 | ||
| @C6 | |||
| | | | ||
|} | |} | ||
Revision as of 17:35, 12 February 2019
Navigation: Documentation / Collective Variables / Nucleic Acids
Distance
Angle
Coordination
Shape
Special
Energy
Algebra
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.
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 | |
| G | @N9,C8,N7,C5,C6,N1,C2,N3,C4 | @C8 | |
| C | @N1,C6,C5,C4,N3,C2 | @C6 | |
| T | @N1,C6,C5,C4,N3,C2 | @C6 |
References
- cite the article