Input files

Secondary structure profile file (*.ss2 file format) is the only mandatory input to the program. Example input file for 2GB1 protein can be found here. Optionally, a starting conformation (in the PDB format) may be provided with -model::pdb flag.

Please note that these input files must be in all-residues representation, even though SURPASS models are shorter by 3 residues

An input SS2 file may be conveniently generated from a PDB file as long as it contains secondary structure information in its header. The following command uses seqc program of BioShell package:

seqc -in::pdb=2gb1.pdb -select:chains=A -in:pdb:header -out:ss2

Output files

After every outer cycle (see options below), surpass_annealing makes an observation of the current state of the simulated system. Typically this means observing energy of the system, various evaluators, topology of a protein, and the coordinates in .pdb file format.

The file provides energy components for every observed frame
The file provides movers acceptance ratio and range
provides various measurements for every observed frame, such as elapsed time, temperature, radius of gyration, crsmd, etc.
The file topology footprint
File contains coordinates of the system recorded at every observation event (file name may be changed with -out:pdb option)