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

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Mon Jun 25 2007 - 07:06:28 CDT

Thank you for the file, Jerome. I have used it as you suggested. The
simulation is running smoothly

-Maria

On 6/24/07, Jerome Henin <jhenin_at_cmm.chem.upenn.edu> wrote:
>
> 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
>
>

-- 
Maria G.
Technical University of Denmark
Copenhagen

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