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

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Sun Jun 24 2007 - 11:37:53 CDT

Maria,
For such cases, you can use a dummy coordinate that is as fast as
possible and does not need any parameters, since it won't do anything.
I attach the file, just copy it to the directory where abf scripts are
and use "abf coordinate dummy".
Jerome

On 6/24/07, maria goranovic <mariagoranovic_at_gmail.com> wrote:
> Thankz you Peter and Subramanian for the comments.
>
> It looks like ABF will be the most straightforward method to use.
>
> But ABF seems to involve using external forces along some reaction
> coordinate besides the constraints that I am interested in . Is that correct
> ? I would like to keep the rest of my system under no external force or
> energy. Can that be done using ABF ? If so, could you please advise me how ?
>
> Thank you again,
>
> -Maria
>
> On 6/21/07, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> > If all you're attempting to do is get the helix formed the easiest and
> > fastest way to do it currently is probably to invoke the abf module and
> > apply dihedral constraints through it; these would be harmonic
> > constraints. If you're feeling more adventurous, the CVS version of namd
> > includes a new feature (extraBonds) that allows you to specify such
> > constraints directly and have them calculated along with other
> > interactions of the applied type; going that route would require getting
> > a cvs account and messing with some new features. Option 3 is also a
> > good one, although you don't seem to like it...
> >
> > As far as speed is concerned, options 1 and 2 will have roughly the same
> > speed since they're doing the force calculations in tcl and not in the
> > (parallelized) namd bonded force evaluation routines. Option 3 and
> > extraBonds should be faster than 1 and 2, and will be equivalent to each
> > other.
> >
> > Peter
> >
> >
> >
> > maria goranovic wrote:
> > > Er.. anyone ?? Help !!!
> > >
> > >
> > >
> > > On 6/19/07, *maria goranovic* < mariagoranovic_at_gmail.com
> > > <mailto: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
> >
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen


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