phi and psi dihedral restraints

From: Neelanjana Sengupta (
Date: Sun Oct 22 2006 - 18:24:24 CDT


I am simulating a peptide, and I want to restrain its phi and psi dihedral
angles to those conforming to an alpha-helix. Since the (CA:nth residue,
C:nth residue, N:(n+1)th residue, CA: (n+1)th residue) make the phi
dihedral, and the (C:n, N:(n+1), CA:(n+1), C:(N+1) ) make the psi
dihedral, I have the following in my restraint input file:

dihe (VAL8, 4, CA) (VAL8, 4, C) (VAL8, 5, N) (VAL8, 5, CA) barr=100 ref=-70
dihe bound (VAL8, 4, CA) (VAL8, 4, C) (VAL8, 5, N) (VAL8, 5, CA) gap=80
low=-120 hi=-67 delta=10
dihe (VAL8, 4, C) (VAL8, 5, N) (VAL8, 5, CA) (VAL8, 5, C) barr=100 ref=-50
dihe bound (VAL8, 4, C) (VAL8, 5, N) (VAL8, 5, CA) (VAL8, 5, C) gap=80
low=-67 hi=-47 delta=10

However, Ramachandran plots show that my peptide is being driven to very
unexpected regions; it is not remaining in the phi:(-80, -67) and psi:(-67,
-47) degrees. Can somebody point out what possibly could be wrong?
Also, am I right in assuming that both restraints can applied together (as
phi and psi involve some common atoms)?

Any suggestions or recommendations are appreciated. Thanks!
Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
Phone: 1-949-824 9921

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