CV:NASBPP: Difference between revisions
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The simple base pair parameters for the A:B base pair. | The simple base pair parameters for the A:B base pair. | ||
''' | '''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 or use 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 from '''A''' base defining origin of y-axis | |||
|- | |- | ||
| ''' | | '''group_d''' | ||
| | | [[Mask format|mask]] | ||
| | |||
| atom from '''B''' base defining end of y-axis | |||
|- | |||
| '''parameter''' | |||
| string | |||
| | | | ||
| | | type of parameter: | ||
|} | |} | ||
''Keys in bold are mandatory.'' | ''Keys in bold are mandatory.'' | ||
Revision as of 16:40, 12 February 2019
Navigation: Documentation / Collective Variables / CV:NASBPP
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Definition
The simple base pair parameters for the A:B base pair.
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 or use 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 from A base defining origin of y-axis | |
| group_d | mask | atom from B base defining end of y-axis | |
| parameter | string | type of parameter: |
Keys in bold are mandatory.