Input fasta file of the target sequence. Must correspond to input.
Dot-bracket secondary structure of the target. Must be the same length as the target fasta. May use []{}<> for pseudoknots. Use . for any regions specified explicitly as starting PDBs, even if those regions are helical.
Input PDB file(s) of RNA (required). (Waters and unrecognized small molecules will NOT be removed)
PDB file containing part of the target model to which to align the simulation, using 4.0 A RMSD constraints.
Native PDB file.
Number of structures to generate:
Number of Monte Carlo cycles to use:
Use the most recently published scoring function for stepwise (recommended)
Use the BETA scoring function currently under active evaluation and development (not recommended)