Re: how to apply restraints for phi and psi for alpha helix regions

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Thu Dec 11 2008 - 13:12:14 CST

Dear Achani,

On Thu, Dec 11, 2008 at 7:42 AM, Achani K. Yatawara
<Achani.K.Yatawara_at_dartmouth.edu> wrote:
> Hi everyone,
>
> Sorry for asking the same question again. I am a new NAMD user and I hope NAMD experts can help me with the following problem.
>
> I want to apply phi and psi restraints for 2 alpha helix regions for initial steps of my simulation.

I suggest you use a CVS version of NAMD which implements the
extraBonds feature, and add extra dihedral angles that you want to
restrain. Your NAMD config file should have:

extraBonds yes
extraBondsFile extrabonds.txt

The extrabonds.txt file will define any extra bonds, angles,
dihedrals, or impropers (copying from an email from Jim Phillips):

# note 0-based indices

# duplicate bonds not allowed
# bond a1 a2 k ref
bond 0 5 10. 6.
bond 5 10 10. 6.

# duplicate angles, dihedrals, impropers OK
# angle a1 a2 a3 k ref
angle 0 5 10 1. 120.
angle 5 10 15 1. 120.
angle 10 15 20 1. 120.
angle 10 15 20 1. 120.

# dihedral a1 a2 a3 a4 k ref
dihedral 0 5 10 15 1. 120.
dihedral 0 5 10 15 1. 120.

# improper a1 a2 a3 a4 k ref
improper 0 1 2 3 1. 0.
improper 0 1 2 3 1. 0.

The VMD plugin ssrestraints, available in the latest alpha versions,
automates the generation of phi and psi dihedral restraints. In your
case, you could do something like:

package require ssrestraints
ssrestraints -o extrabonds.txt -sel {resid 1 to 10}

to generate an extrabonds file with an extra dihedral for each phi and
psi angle in your selection. By default, the equilibrium value is
taken from the original structure, but you can specify the flag -ideal
to use ideal values for an alpha helix, for example. Type ssrestraints
for more usage information.

Please note that the force constant is defined in the same way as in
the parameter file. For instance, for bonds, V=kx^2 (and NOT
0.5*kx^2).

Cheers,
Leo

-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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