On Tue, Apr 06, 2010, Andrew Olson wrote:
> So the rk2 and rk3 values are in the restraint file like this (from tutorial)
>
>
> # 632 atoms read from pdb file gcg_b.amb.pdb.
> # 1 GUA GAMMA: (1 DG5 O5')-(1 DG5 C5')-(1 DG5 C4')-(1 DG5 C3') -20.0 140.0
> &rst iat = 2, 3, 6, 26,
> r1 = -21.0, r2 = -20.0, r3 = 140.0, r4 = 141.0,
> rk2 = 32.0, rk3 = 32.0, &end
>
> # 3 GUA GAMMA: (3 DG O5')-(3 DG C5')-(3 DG C4')-(3 DG C3') 0.0 120.0
> &rst iat = 65, 66, 69, 89,
> r1 = -1.0, r2 = 0.0, r3 = 120.0, r4 = 121.0,
> &end
>
> # 4 THY GAMMA: (4 DT O5')-(4 DT C5')-(4 DT C4')-(4 DT C3') 0.0 120.0
> &rst iat = 98, 99, 102, 121,
> r1 = -1.0, r2 = 0.0, r3 = 120.0, r4 = 121.0,
> &end
>
> My question is, are these rk2 and rk3 force constants for only that
> residue or are they for every residue? I saw a previous post
You should set LISTIN=POUT in the redirection section; that gives details of
all the restraints as they are read in; use this to see if you are getting
what you want or not. It's been a long time since I have used these programs.
....dac
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Received on Tue Apr 06 2010 - 15:30:05 PDT
