AMBER Archive (2009)

Subject: [AMBER] QQD psuedoatom restraints

From: Titus, Jamie (bairdje) (BAIRDJE_at_UCMAIL.UC.EDU)
Date: Fri May 29 2009 - 09:02:31 CDT

Hello AMBER users,

I am refining my NMR structure in AMBER and encountering the following:

An example of a psuedoatom restraint in my calculation:

# 13 LEU QQD 16 LEU QQD 3.61 (#peak 191)
 &rst
  ixpk= 191, nxpk= 0, iat= 226, 277, r1= 1.30, r2= 1.80, r3= 3.61, r4= 4.11, &end

the contents of map.DG-AMBER pertaining to this restraint (used by makeDST_RST):

PSEUDOC QQD = CG 2.2

and the following violation in the POUT file:

CG LEU 13 -- CG LEU 16: 5.015 3.610 1.405 23.094 d 191: 0

Which implies to me that AMBER is attempting to enforce a 3.61 angstrom distance between the CG
atoms of the two leucine residues. The line in the map.DG-AMBER file implies to me that the
restraint between two QQD atoms would be extrapolated to the two CG atoms PLUS 2.2 Angstroms. Is
this correct? And if so, why is the POUT file reflecting that AMBER is enforcing the original
3.61 angstrom restraint and that it is violated?

Thanks for your help.

Jamie

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