PROFASI  Version 1.5
Using an arbitrary measurement as a restraint

ProFASi measurements module provides a large number of measurements such as RMSD, radius of gyration, secondary structure etc. If desired, any of those measurements can be used as a pseudo-energy term to restrain the simulation. While this does not make much sense for a folding simulation of one protein, in many studies some form of restraints are useful. For instance, if we want to study the binding of one small peptide with a large protein, large scale conformational changes of the big protein are not the prime objects of the study. A free MC simulation will normally unfold the big protein and try to explore its entire conformation space – that's what an MC run is supposed to do, i.e., explore conformation space without being trapped in any minimum for ever. One way to keep a protein near a given structure is to use the RMSD of the current state with the reference state as an energy term. Larger the RMSD, larger the penalty.

Instead of anticipating all possible measurements which someone might want as an energy term in a study, we provide a generic mechanism to use just about any measurement done during a run as an energy term. The syntax looks like this in the settings file:

  force_field FF08Rg=FF08+Extras:ObsEnergy(obs=rg,scale=50)

This sets up a force field that is the sum of the default force field and a term that is 50 times the value of an observable called "rg". Presumably the settings file also has a line creating a measurement called "rg":

  new_obs Rg rg of_chain 0

The name "rg" used is the alias given to the measurement by the user, not the name of the class. Note that the above scale factor of 50 on the radius of gyration is just a random example. With this value, almost any protein with 30 residue or more is likely to turn into a nice ball with hardly any secondary structure.

Energy terms themselves are measurements in ProFASi. So, it is possible to generate nonsense by "connecting" the new ObsEnergy object to itself!

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