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? Thanks, -- **************************************** Neelanjana Sengupta, PhD student Dept. of Chemistry Univ. of California-Irvine Irvine, CA 92697 USA Phone: 1-949-824 9921 email: sengupta_at_uci.edu ****************************************
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