From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Sun Oct 22 2006 - 18:24:24 CDT
Hi,
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
USA
Phone: 1-949-824 9921
email: sengupta_at_uci.edu
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