AMBER Archive (2009)

Subject: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint?

From: liu junjun (ljjlp03_at_gmail.com)
Date: Sun Feb 01 2009 - 01:51:39 CST

Hello everybody,

I am trying to put distance restraint on a pair of bonded atoms. I
defined the two atoms, which are actually bonded to each other in the
intial strcture, in the NMR distance restraint file but it looks like
the restraint force is not applied on the distance I defined. I set a
long distance (3 angstrom) as the target and a huge force constant in
distance restraint input file, which should end up with huge penalty
on the distance I defined. But the restraint output file does not
generate any penalty and the minimized structure does not show any
changes on the distance I defined. The format for input files should
be OK because I successfully restrained other distances of non-bonded
pair of atoms with similar input files. I am wondering if NMR distance
restraint can not be used on bonded atoms or not? If the answer is no,
then can someone give me a suggestion on restraining a specifically
pair of bonded atoms? BTW, I am using AMBER9.

here is my input files:
=== sander input ====
# Control section
 &cntrl
 ntpr = 5,
 cut = 10.0,
 ntb = 0,
 maxcyc = 10,
 ncyc = 20,
 drms=0.05,
 ntr = 0,
 imin = 1, ibelly=1,
 bellymask="@C32 < @20.0 & !(@C32|:197_at_OG)"
 nmropt=1,ipnlty=1
 &end
 &wt type='REST',istep1=1,istep2=100000,
   value1=1.0, value2=1.0,&end
 &wt type='END' /
  LISTOUT=RST.out
  DISANG=dis.RST
=================

======= NMR distance restraint file ====
 &rst IRESID=0, iat=8385,8384, r3=3.04,
   r4=3.1, r1=3.04, r2=3.04, rk2=8000, rk3=8000,/
 &end
===============================

======= output file for NMR distance restraint ==========
  ------------------------------------------------------------------------------

 Final Restraint Analysis for coords: min1.rst

 Restraints, deviations, and energy contributions: pencut = 0.10

 ------------------------------------------------------------------------------
     First atom Last atom curr. value target deviation penalty
 ------------------------------------------------------------------------------
 ------------------------------------------------------------------------------
====================================

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