AMBER Archive (2008)

Subject: Re: AMBER: makeDIST_RST computation of r3 value with IAT < 0

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri Dec 05 2008 - 10:45:20 CST

On Wed, Dec 03, 2008, Ryan Pavlovicz wrote:
>
> While preparing an NMR restraint file with an 8 column input file to the
> makeDIST_RST program, i notice that the r3 values that i provide are altered
> in the cases of IAT(1) < 0 or IAT(2) < 0. I presume this is done to
> compensate for the distance averaging done during group assignment, but can
> anyone describe how makeDIST_RST determines the r3 output value based on the
> input? I cannot find this described in the AMBER User Manual. Thanks a
> lot,

The method depends on whether the -nocorr flag is set (type "makeDIST_RST
-help" for a list of flags.) If this flag is not set, an r**-6 weighted
average is made of the individual distances. The calculation is done in the
correct_upperbound() routine in makeDIST_RST.c.

....dac

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