Dihedral restraints do not work

From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Tue Mar 20 2007 - 10:44:10 CDT

Hi NAMD users,

I seem to consistently have a problem in applying dihedral restraints.
My aim is simple: in a simulation, I want to set the (phi,psi) angles of a
small peptide to desired values. For that, I make a restraint file (call it
r.inp) as follows, setting all the (phi, psi) angles:

urestraint {
dihe (VAL8, 2, N) (VAL8, 2, CA) (VAL8, 2, C) (VAL8, 3, N) barr=100 ref=-30.0
dihe (VAL8, 3, C) (VAL8, 4, N) (VAL8, 4, CA) (VAL8, 4, C) barr=100 ref=-57.0
dihe (VAL8, 3, N) (VAL8, 3, CA) (VAL8, 3, C) (VAL8, 4, N) barr=100 ref=-30.0
dihe (VAL8, 4, C) (VAL8, 5, N) (VAL8, 5, CA) (VAL8, 5, C) barr=100 ref=-57.0
mcti {
        task = stepup
        equiltime = 1ps
        accumtime = 1ps
        numsteps = 5
        print = 1ps

and my simulation input file includes the foll:,
freeEnergy              on
freeEnergyConfig     r.inp
Now, this does not work. My (phi, psi) values do not change on using the
restraint. Using dihedral bounds, in the form of,
dihe bound (VAL8, 3, C) (VAL8, 4, N) (VAL8, 4, CA) (VAL8, 4, C) gap=100
low=-58 hi=-55 delta=5
does not help.
I am at my wit's end now... Can someone please point out what's missing?
Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
Phone: 1-949-824 9921
email: sengupta_at_uci.edu

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