Re: Changing loop to helix: restraining about 20 dihedral angles

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Thu Jun 21 2007 - 01:33:30 CDT

Er.. anyone ?? Help !!!

On 6/19/07, maria goranovic <mariagoranovic_at_gmail.com> wrote:
>
> 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
>

-- 
Maria G.
Technical University of Denmark
Copenhagen

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