CV:NASBPP: Difference between revisions
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Navigation: [[Documentation]] / [[Collective Variables]] / [[CV:NASBPP]] | Navigation: [[Documentation]] / [[Collective Variables]] / [[Nucleic Acids]] / [[CV:NASBPP]] | ||
---- | ---- | ||
{{CVS}} | {{CVS}} | ||
===Definition=== | ===Definition=== | ||
The simple base pair parameters for the A:B base pair | The simple base pair parameters for the A:B base pair fully compatible with the 3DNA definition. | ||
'''IMPORTANT:''' It is critical that the A and B bases are not separated during simulation due to imaging of DNA chains into the simulation box. Use ether topjoinmol from CATs to merge both chains into a single molecule or use the correct value of iwrap in sander or pmemd. | |||
===Specification=== | ===Specification=== | ||
| Line 27: | Line 26: | ||
| [[Mask format|mask]] | | [[Mask format|mask]] | ||
| | | | ||
| atoms for the base | | atoms for the base '''A''' ring | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| '''reference_a''' | | '''reference_a''' | ||
| string | | string | ||
| | | | ||
| name of file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group '''group_a | | name of the file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group '''group_a''' | ||
|- | |- | ||
| '''group_b''' | | '''group_b''' | ||
| [[Mask format|mask]] | | [[Mask format|mask]] | ||
| | | | ||
| atoms | | atoms for the base '''B''' ring | ||
|- style="vertical-align: top;" | |- style="vertical-align: top;" | ||
| '''reference_b''' | | '''reference_b''' | ||
| string | | string | ||
| | | | ||
| name of file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group '''group_b''' | | name of the file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group '''group_b''' | ||
|- | |- | ||
| ''' | | '''group_c''' | ||
| | | [[Mask format|mask]] | ||
| | | | ||
| | | atom defining origin of y-axis | ||
|- | |||
| '''group_d''' | |||
| [[Mask format|mask]] | |||
| | |||
| atom defining end of y-axis | |||
|- | |||
| '''parameter''' | |||
| string | |||
| | |||
| type of parameter (one of): shear, stretch, stagger, buckle, propeller, opening | |||
|- | |||
| skip_mass_test | |||
| logical | |||
| .false. | |||
| if .true. it does not control atom masses between the system and loaded reference structures | |||
|} | |} | ||
''Keys in bold are mandatory.'' | ''Keys in bold are mandatory.'' | ||
Latest revision as of 17:09, 12 February 2019
Navigation: Documentation / Collective Variables / Nucleic Acids / CV:NASBPP
Distance
Angle
Coordination
Shape
Special
Energy
Algebra
Definition
The simple base pair parameters for the A:B base pair fully compatible with the 3DNA definition.
IMPORTANT: It is critical that the A and B bases are not separated during simulation due to imaging of DNA chains into the simulation box. Use ether topjoinmol from CATs to merge both chains into a single molecule or use the correct value of iwrap in sander or pmemd.
Specification
Section name: NASBPP
| Key | Type | Default | Description |
| name | string | unique CV name | |
| group_a | mask | atoms for the base A ring | |
| reference_a | string | name of the file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_a | |
| group_b | mask | atoms for the base B ring | |
| reference_b | string | name of the file with the reference structure in the XYZ format, the structure must have the same number of atoms as the group group_b | |
| group_c | mask | atom defining origin of y-axis | |
| group_d | mask | atom defining end of y-axis | |
| parameter | string | type of parameter (one of): shear, stretch, stagger, buckle, propeller, opening | |
| skip_mass_test | logical | .false. | if .true. it does not control atom masses between the system and loaded reference structures |
Keys in bold are mandatory.