Currently i am using the tleap in amber tools to generate a PDB using only dihedral angles. Is it possible to generate a PDB/Model using only dihedral angles and the sequence, just like amber tools. I have read the whole manual, but didn't get anything useful. The only way you can restrain your model is using restrain file .rsr, which i really don't know how to generate from dihedral angles.
On 4/27/14, 9:07 PM, Harinder Singh wrote: > Currently i am using the tleap in amber tools to generate a PDB using > only dihedral angles. Is it possible to generate a PDB/Model using only > dihedral angles and the sequence, just like amber tools.
No. Modeller is designed to build comparative models, and works in Cartesian space, not internal coordinates. You could certainly add restraints on individual dihedral angles and then optimize, but it wouldn't be the most efficient way to generate such a model.
Ben Webb, Modeller Caretaker
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Harinder Singh -
Modeller Caretaker