AMBER Archive (2007)

Subject: Re: AMBER: torsion angle penalty calculation

From: David A. Case (case_at_scripps.edu)
Date: Wed Jan 03 2007 - 10:54:33 CST

On Wed, Jan 03, 2007, Mike Summers wrote:
>
> I'm trying to fix torsion angles using torsion restraints
> in an NMR restraint file.
>
> FROM THE RESTRAINT FILE:
> #####################################
> # C6-C7-N1-C8
> &rst
> rk2=10000.0, rk3=10000.0, ialtd=0,
> iat=2273,2274,2263,2275, r1=-180.10, r2=-180.05, r3=-179.95, r4=-179.90, /
> #####################################
>
>
> When I look at the output file, it appears that the penalty
> for the torsion angle restraints is being calculated differently
> from the NOE-distance penalties, even though IPNLTY is set to 1.

First, the manual is misleading about IPNLTY: this applies only to NOESY
volume or chemical shift restraints. It is ignored for distance and torsion
restraints: there the potentials listed on pp. 180-181 are applied. I will
prepare an erratum to explain this correctly.

>
> Restraints, deviations, and energy contributions: pencut = 0.00
>
> ------------------------------------------------------------------------------
> First atom Last atom curr. value target deviation penalty
> ------------------------------------------------------------------------------
> C7 cap 146 -- N1 cap 146: -180.156 -180.050 0.106 0.025 t
>
> I assume it is the penalty that is used during the structure calculations.
> If so, is there a flag or parameter that allows the penalty for torsion angles
> to be calculated linearly with deviation, or better yet, to scale at a much
> greater rate than linear? The torsion angles are varying significantly during
> the calculations, and I'd like to keep them relatively rigid.

It looks to me like the program is doing the right thing: in the example
above, you have a deviation of .106 degrees = .0018 radians. The parabolic
penalty is then 10000 * (.0018)^2 = 0.034 kcal/mol. Since the current
value is actually below r1, the potential flattens out (to linear, rather than
parabolic), so it is even smaller that the parabolic value would have been.

I think what you want to do is to make the difference between r1 and r2 bigger
(also between r3 and r4). Since you want to keep the torsions rigid, try
setting r1 to -200 (say) and r4 to -160. This will make the penalty bigger
for larger deviations. For your case, a 1 degree deviation would then have
a 3 kcal/mol penalty, and a 5 deg. deviation would have a 76 kcal penalty, so
you should not see deviations larger than a few degrees.

[It is also no problem to set r2=r3; then you have a simple parabolic
potential = rk2*( curr - 180)^2, which is easy to calculate by hand to check
what the program is doing.]

If you need to constrain things even more tightly, you would have to increase
the values of rk2 and rk3 accordingly. But you might run into problems with
the MD algorithm if the constraint gets really strong.

...good luck....dac

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