PROFASI  Version 1.5
Simulations with distance restraints

Using distance restraints in a simulation follows exactly the same syntax as does the use of dihedral restraints (See Restraining simulations with a torsional angle potential ). The following one line in the settings file will set up a new energy term according to the restraints specified in the XML configuration file dist_restr.xml .

force_field FF08DR=FF08+Extras:DistanceRestraints(dist_restr.xml)

The procedure for specifying the restraints in the command line is the same as for the dihedral restraints.

Configuring distance restraints using an XML file

The distance restraints energy term must be configured so that it knows which distances to use and what to do with them. The XML configuration file should have the following format:

Example

The following XML file configures 5 distance restraints:

<distance_restraints>

<formatted_data>

<format name="restraint" type="$3">
  <atom1>$1</atom1>
  <atom2>$2</atom2>
  <parameters>
    <mean>$4</mean>
    <weight>$5</weight>
  </parameters>
</format>

<data>
0/0/GLY/_CA_ 0/15/GLU/_CA_ quadratic 5.5 3.0
0/1/GLU/_CA_ 0/14/THR/_CA_ quadratic 5.5 3.0
0/2/TRP/_CA_ 0/13/VAL/_CA_ quadratic 5.5 3.0
0/3/THR/_CA_ 0/12/THR/_CA_ quadratic 5.5 3.0
0/4/TYR/_CA_ 0/11/PHE/_CA_ quadratic 5.5 3.0
</data>

</formatted_data>

</distance_restraints>

In connection with dihedral restraints, we introduced the template interpretation capacity of the ProFASi XML module. The above is another example. Here the tabular data to be re-cast as a series of XML nodes appears inline inside a special tag data. The format tag is used to interpret the contents of the data tag. Here we also introduce how to specify the functional form by giving a type attribute to the auto-generated restraint nodes.

The atoms are specified through their chain, residue number, residue type, and atom label. The labels are 4 characters wide. Spaces in the label should be replaced by underscores. It is important to have the labels correct. It is " CA " (and therefore "_CA_" above), and not "CA__" for C-alpha.

Several alternative forms are available for the functional form. In place of quadratic, one could write "power_law", "flattened_power_law" or "gaussian" to use the functions represented by prf::PowerLawRestraint, prf::FlattenedPL and prf::GaussianRestraint respectively.

See Also
Restraining simulations with a torsional angle potential

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2