Reply To: AbinitioRelax under different directories without -constant_seed -jran flag

[Anonymous]

Try out:file:silent_struct_type instead of out:silent:silent_struct_type, to fix your first problem. I don’t know if it will affect the NaNs.

The “max cycles exceeded” error is an internal error in gradient-based energy minimization, not an error in the monte carlo cycles of the abinitio protocol. There’s no way to alter the number of cycles in minimization – if you get this error it means you’re in an unminimizeable portion of the energy landscape and the solution is to let the program go on to its next fragment move, etc.

Altering the number of cycles in abinitio will not affect this error. Abinitio’s number of monte carlo cycles is scaled automatically by the length of the protein and does not need to be altered externally. Nstruct alters the number of result structures, not their length.

If you have a particularly large protein, keep in mind that Rosetta isn’t that good with those. It does better at folding individual domains than large proteins.