The default parameters used by LINUS may be changed by including one of the following entries in the LINUS run file linus.py.
Instructions for overriding the parameters listed below are described in the Sample LINUS Run Files section.
The default simulation parameter values are:
beta= 2.0, beta = 1/RT. A value of 2.0 approximates 25 deg C in the context of LINUS.
numcycle= 1000, A cycle is N-2 moves where N is the number of residues in the polypeptide.
A move consists of choosing, at random, one of four secondary structure phi, psi combinations and applying these to residue i, i-1 and
Residue i may be any residue 2 to N-1 and is chosen randomly for each move.
numsave= 10, Save a structure every 10 cycles.
trials= 1, Number of simulation trials to run. See next two parameters which relate to this.
updateweights= 0, Count fraction of different secondary structure fractions at end of trial and weight choice of secondary structures for next trial according to fraction; yes, 1; no, 0
reset_conformation= 0, Reset conformation at end of trial back to original input conformation (usually extended); yes, 1; no, 0
write_rc= 0, Write out a file containing a mesostate list for each accepted conformation (this can be large); yes, 1; no, 0
The default H-bond parameters are:
use_hbond= 0, Use backbone to backbone hydrogen bonds: yes, 1; no, 0
use_sidechain_hbond= 0, Use sidechain to backbone hydrogen bonds: yes, 1; no, 0
hbond_distance= 3.5, Limit distance for H-bond score to be its maximum value (as defined in hbond_score_short).
hbond_probe= 1.5, Score scales to 0 at distance hbond_distance + hbond_probe (3.5 + 1.5 = 5.0).
hbond_score_short= 0.5, Score at <= hbond_distance distance for H-bonds to residues with sequence separation
<= 6 residues.
hbond_score_long= 1.0, Score at <= hbond_distance distance for H-bonds to residues with sequence separation > 6 residues. There is no scaling for these H-bonds, the score goes to zero if the distance is larger than hbond_distance.
hbond_torsion= 140.0, Out of plane dihedral Oj - Ni - CAi - Ci-1 minimum (absolute value) for H-bond to form.
This insures that N-H...O hydrogen bonds are +/- 40 degrees from directly in line with the N-H vector.
sidechain_hbond_distance= 3.5, Limit distance for side chain donor to back bone acceptor. There is no switching
for these H-bonds, the score is zero beyond this limit.
sidechain_hbond_score= 1.0, As above for side chain donor to back bone acceptor.
sidechain_hbond_torsion= 140.0, As above.
hbond_winmin= 2, Minimum sequence separation between two residues that can participate in backbone/sidechain acceptor to backbone donor hydrogen bonds.
hbond_winmax= 6, Maximum sequence separation between two residues that can participate in backbone/sidechain acceptor to backbone donor hydrogen bonds. Insures local interactions only.
use_hbs_local=0,,Test if the backbone N and O atoms in moveset residues (3 residues) are hydrogen bonded or accessible to water.
If they are not hydrogen bonded after the move, penalize the conformation with a positive score of 1.0. Default is off.
The default contact parameters are:
use_contact= 0, Use hydrophobic contacts; yes, 1; no, 0.
contact_probe= 2.8, Contact scored only if distance between the surfaces of designated atoms for each of the two residues is <= contact_probe distance.
contact_winmin= 2, Minimum sequence separation between two residues that can participate in contact energy calculations.
contact_winmax= 6, Maximum sequence separation between two residues that can participate in contact energy calculations.
contact_scale= 1.0, Multiplier of the contact energy term.
The default torsion parameters are:
use_torsion= 0, Penalizes non-GLY residues if they assume positive phi values and rewards GLY for the same.
Default is off.
The default solvation parameters are:
use_chasa= 0, Estimates the solvation energy using the Conditional Hydrophobic Acessible Surface Area algorithm (CHASA).
Default is off. (Warning: This algorithm is slow).
The default conformational weights are:
Set sampling weights for specified move type and specified list of residues.
These five values define the "smart move set" for Monte Carlo trial moves.
The last argument is a list of residues; it could be "all" for all residues, "1, 5, 9" for residues 1, 5, and 9, or " 'gly', 'pro' " for all gly and pro residues (notice single quotes).
See the Examples section for an example of a LINUS run file with a random (non-smart) move set.