Changing loop to helix: restraining about 20 dihedral angles

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Tue Jun 19 2007 - 10:59:16 CDT

I want to restrain about 20 random coil contiguous residues to a helical
conformation, while leaving the rest of my protein intact. According to the
documentation, there are at least three ways to do this:

1. Using a tcl forces script, like the one recommended in the manual.
http://www.ks.uiuc.edu/Research/namd/2.6b1/ug/node32.html#SECTION00096700000000000000.
However, the script may get slightly tedious for 20 operations.
2. Using the restraining options in the free energy methods. But here, the
free energy routines will need to be invoked, which might slow the overall
calculation, because an unnecessary derivative will be calculated each step.
3. Modify the psf to define new residue types and new dihedrals (I want to
avoid this).

My questions:

a. Which is the recommended method in terms of saving of computational time
?
b. In the free energy method, is the dihedral restrained harmonically
throughout the simulation like it would be in the TCL forces script ?
c. In terms of added potentials and forces, is the effect of using a tcl
forces script or a restraint in a free energy calculation similar to that,
say of using standard harmonic constraints in NAMD ?

My goal is to investigate the effect of the coil-helix transformation on the
loop region next to the protein region in question.

Any suggestions please ? All partial answers are also welcome :)

-Maria

-- 
Maria G.
Technical University of Denmark

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