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