AMBER Archive (2003)

Subject: Re: IR6 and makeDIST-RST

From: David A. Case (case_at_scripps.edu)
Date: Sun Jun 01 2003 - 19:14:04 CDT

On Sat, May 24, 2003, Francisco Blanco wrote:
>
> I think that I am missing something about the use of ir**-6 averaging for
> distance restraints applied to groups in sander NMR structure refinement.
> I used them for non-stereospefically assigned protons and
> methyls. My understanding is that with this treatment no pseudoatom
> correction is necessary. However, when I use the makeDIST_RST program and
> the map.DG-AMBER (modified to get the six protons of isopropyl groups), I
> get the distances corrected, something like this:

The distances do get modified to match the r**-6 averaging; in the (somewhat
obsolete) language of the field, this modification is not a "pseudoatom"
correction, however.

Generally speaking, if you have a distance that would be appropriate for
a single-proton peak, you should accept the modification for the r**-6
averaging.

>
> When try the option -nocorr of makeDIST_RST, I get the upper bound
> distance set to zero:
>
> #
> # 3 LEU HA 3 LEU QD1 5.00 1.00E-01 (#peak 2867)
> &rst
> ixpk= 2867, nxpk= 0, iat= 34, -1, r1= 1.30, r2= 1.80, r3= 0.00, r4=
> 0.50,
>
> rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
> igr2= 41, 42, 43, 45, 46, 47,
> &end
> #
> 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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