AMBER Archive (2003)

Subject: IR6 and makeDIST-RST

From: Francisco Blanco (fblanco_at_cnio.es)
Date: Sat May 24 2003 - 14:15:29 CDT

Hi:

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:

#
# 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= 6.74, r4=
7.24,

      rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
 igr2= 41, 42, 43, 45, 46, 47,
 &end
#

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
#

Any comments are appreciated. Thanks 

-- 
Francisco Blanco
NMR group, Structural and Computational Biology Programme
Centro Nacional de Investigaciones Oncológicas
Melchor Fernández Almagro 3, 28029 Madrid, Spain
Phone: 34 91 2246983  Fax: 34 91 2246976      www.cnio.es