Restraints on pseudo atoms

pseudo.top demonstrates the use of a restraint between a real atom and a pseudo atom. This input file should work with Modeller 6v2 or later.

pseudo-rsr-example.tar.gz

Files: pseudo.top pseudo.atm pseudo.rsr pseudo.log pseudoout.atm README

The input file pseudo.top does the following:

• READ_MODEL reads pseudo.atm, which defines five real atoms - four of these are positioned at the corners of a square in the xy plane, with center 0,0,0, and the fifth is off in space.
• READ_RESTRAINTS then reads pseudo.rsr, the first line of which defines a pseudo atom:

P 6 1 4 1 2 3 4

This reads, in order, as 'define a pseudo atom (P) as atom number 6, of type 1, which is a gravity center of 4 atoms, of numbers 1, 2, 3 and 4'. See http://salilab.org/modeller/6v2/manual/node99.html for more details. Note that the atom number (6) of the pseudo atom must be greater than the number of real atoms in the model (5 in this case).
The second line defines an actual restraint in the MODELLER format. See http://salilab.org/modeller/6v2/manual/node98.html for more details:

R 3 1 1 27 2 2 0 5 6 0.0 0.100

These fields map to:

• R: define a restraint
• 3: of form '3' (harmonic potential, table 2.2)
• 1: of modality '1' (ignored in this case)
• 1: using feature '1' (distance, table 2.3)
• 27: report energy in group 27 (Distance restraints 5, table 2.4)
• 2: restrain 2 atoms
• 2: the restraint takes two parameters (fmean and sigma, table 2.2)
• 0: ignored
• 5,6: act on real atom 5 and pseudo atom 6
• 0.0: fmean is zero
• 0.100: sigma (standard deviation, strength of the restraint) is 0.100
• With this restraints file read, we have created a harmonic restraining potential between real atom 5 and the gravity center of atoms 1, 2, 3 and 4, which, since fmean is zero, will tend to force atom 5 to coexist with this gravity center. The subsequent optimization yields a file pseudoout.atm which demonstrates this.

It is straightforward to add restraints of this type to a comparative modeling run - see for example, http://salilab.org/modeller/6v2/FAQ.html#9