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
stating that one gets many angle restraint violations running amber but not when cyana and the suggestion was to increase the force constants ( to larger values). My understand is that
this will cause some angles to not be violated, is this right. Do you have to put the rk2 and rk3 values under those residues or are they read from the top line. Thanks for your help.
________________________________
From: case <case.biomaps.rutgers.edu>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Sat, April 3, 2010 5:18:00 PM
Subject: Re: [AMBER] makeANG_rst values
On Sat, Apr 03, 2010, Andrew Olson wrote:
> I am wondering if its possible to change some value in the makeANG_rst
> so that rk2 and rk3 always come up as something like 10 every time
> instead of 2? If so, where in the file do i change, i looked over it
> but cannot seem to locate where im to change it. Thanks
You can edit K_FORCE_LB and K_FORCE_UB in the source file
to change the default.
...dac
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Received on Tue Apr 06 2010 - 14:30:05 PDT
