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latticesim.pl
Usage
usage: latticesim.pl [options] seqFile
options: [-chain file | -rnd | -pdb file] [-g gridsize]
[-par tsteps=val,ncycle=val,icycle=val,
stiff=val,short=val,central=val,kdcore=val]
[-l force min:max[=min:max ...]]
[-d force res1:res2[=res1:res2 ...]]
[-sa temp] [-const temp]
[-norun]
Description
This script provides an interface for running
low resolution lattice-based protein simulations with MONSSTER.
It creates all necessary input files and runs the MONSSTER program
mfold in the current directory.
The only required argument is a sequence file in MONSSTER
format that can be generated with <docmark>genseq.pl</docmark>.
By default or when -rnd is specified a random chain
is generated as the starting configuration. The option -g
can be used to provide the grid size used in the MONSSTER program.
If this option is not given a default value of 100 is used.
A specific starting configuration can be
specified either directly with -chain in MONSSTER chain
format or by providing a PDB file with -pdb that is
used to generate a chain.
For fragment/loop modeling the option -l can be used
to specifiy ranges of residues that are simulated fully flexible
while the other surrounding residues are restrained according
to the force constant specified. See genrestr.pl
for an explanation how the restraint list is generated.
If -l is used along with the -pdb option
the input chain is generated from the PDB file only for
residues outside the list in the argument of -l
with random positions for the flexible fragment residues.
During fragment/loop modeling a complete starting conformation
for all residues can only be provided in form of a
MONSSTER chain file by using the -chain option.
The option -d can be used to provide residue-residue
distance restraints that may be available from known
disulfide linkages or other information about residue-residue
contacts. This option is particularly useful for structure
predictions starting from random configurations by limiting
the search space significantly.
Two main modes are available for lattice simulations: Simulated
annealing and constant temperature. During simulated annealing
the temperature is decreased continuously at each temperature
step from an initially high value to room temperature. MONSSTER
uses an intrinsic temperature scale where 1.0 corresponds
approximately to room temperature. Typical simulated annealing
runs start at temperatures between 2.0 and 2.5. The option
-sa is used to
select simulated annealing and provide the initial temperature.
Constant temperature simulations are selected with -const
followed by the desired temperature in the same units. This option
also changes default values for the number of temperature steps to
1 and potential scaling of the centrosymmetric potential to 0.5.
By default simulated annealing starting at 2.5 is performed.
Additional options can be specified with -par as a list
of hash-type key/value pairs. A number of parameters are available
to specify the length of simulation cycles:
tsteps selects the number of temperature
steps. This affects the rate of cooling during simulated annealing
but may be set to 1 for constant temperature simulations. The default
value is 10. ncycle specifies the number of cycles at
each temperature step (20 by default) and icycle specifies
the number of Monte Carlo moves per cycle (50 by default).
For selective scaling of specific terms in the force field the following
options (specified with -par) are available:
central sets scaling of the centrosymmetric potential
(default: 0.25) that is used to favor more compact structures over
extended forms. This is helpful if simulations are started from
random chains but may be reduced for simulations of already compact
conformations to avoid a bias towards spherical and too compact
structures.
The parameter stiff controls the scaling of a
generic potential term (default: 1.25) favoring the formation of regular
protein secondary structure elements. For loop modeling reduction of
this potential term may be beneficial.
short determines scaling of short range interactions (default: 0.5)
that depend on the type of secondary structure elements provided in the
sequence file. Increasing this potential term may be useful to increase the
bias towards known secondary structure.
kdcore controls the rate of hydrophobic collapse. The default
value of 0.9 results in relatively rapid collapse to compact structures
with hydrophobic cores. Reduction of this value up to 0.1 results in
more realistic sampling of the folding landscape but with a lower
yield of near-native structures in simulated annealing runs.
Finally, the -norun option can be given to request only a setup
of all necessary files to run MONSSTER without actually calling the
program to start the simulation.
Options
- -help
- usage information
- -chain file
- initial structure from SICHO chain file
- -rnd
- initial structure generated as random chain
- -pdb
- initial structure generated from PDB file
- -g gridsize
- grid size (should match MONSSTER program)
- -par name=value,...
- simulation parameters
- -l force min:max[=...]
- limit sampling to residue range while restraint force is applied to other residues
- -d force res1:res2[=...]
- residue-residue restraints
- -sa temp
- simulated annealing run from given temperature to 1.0
- -const temp
- constant temperature run
- -norun
- prepare input files but do not actually run simulation
Examples
latticesim.pl 1vii.seq
runs a simulated annealing lattice simulation starting from a random
configuration with default simulation parameters
latticesim.pl -l 50.0 10:21 -pdb 1vii.exp.pdb -const 1.0 -par ncycle=100 1vii.seq
runs a constant temperature lattice simulation at approximately room temperature (1.0 in
MONSSTER temperature units). The initial chain is generated from 1vii.exp.pdb with random
positions for residues 10 through 21. During the simulation residues below 10 and above 21 are
restrained with a variable force constant up to 50.0 (in internal MONSSTER energy units).
The -const option for constant temperature automatically selects a single temperature step.
Finally -opt ncycle=100 increases the number of cycles to 100.
latticesim.pl -sa 2.0 -d 5.0 10:34=19:26 -chain 1vii.exp.chain 1vii.seq
runs a simulated annealing lattice simulation starting at a temperature of 2.0 (internal
MONSSTER units). The input chain is taken from a chain file. Distance
restraints with a force constant of 5.0 (internal units) are set between residues 10 and 34
and 19 and 26.