CV:NASBPP: Difference between revisions
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{{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 or use correct value of iwrap in sander or pmemd. | '''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=== | ||
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| [[Mask format|mask]] | | [[Mask format|mask]] | ||
| | | | ||
| atom | | atom defining origin of y-axis | ||
|- | |- | ||
| '''group_d''' | | '''group_d''' | ||
| [[Mask format|mask]] | | [[Mask format|mask]] | ||
| | | | ||
| atom | | atom defining end of y-axis | ||
|- | |- | ||
| '''parameter''' | | '''parameter''' | ||
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| | | | ||
| type of parameter (one of): shear, stretch, stagger, buckle, propeller, opening | | 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.'' | ||