AMBER Archive (2003)

Subject: AMBER:

From: wangf2 (feng.wang.1_at_vanderbilt.edu)
Date: Thu Oct 30 2003 - 10:00:15 CST

Hi, everyone:

I was wondering if anyone can clear this up for me. Could dipolar couplings
between atoms through three bonds be used in NMR refinement in AMBER or not? I
had some problems using H3'P dipolar couplings in DNA annealing. I checked my
annealing protocol and files with dipolar couplings (variables and format)
again and again but could not find the error. What I noticed is that the
examples in the manual used DC between atoms directly bonded, so I wondered if
the dipolar couplings between atoms through several bonds could be used or
not. If those DC could be used, could anybody here help me to find the error?
I was stuck here for a really long time.

What I did
(1)in the annealing protocol, I changed nmropt value to 2 and add the
DIPOLE=z_x8_dc.rst
(2)in dc.rst, I even add a test line #########test at the beginning

What I obtained at the end of the output file
-------
 Alignment info will be read from file: z_x8_dip.rst
 Here are comments from the alignment input file:
 ##############test

 namelist reports error reading &align
-------

It looks like that the system is directing to the DC restraints file and then
stuck there.

Any suggestion would be highly appreciated.

Feng

This is the file with DC restraints.
##############test
 &align
  ndip=20, dcut=-1.0, gigj=5.5856*2.2632,
  s11=53.892, s22=98.521, s12=-60.696, s13=7.2681, s23=33.074,
  id(1)=57, jd(1)=62, dobs(1)= 0.771,
  id(2)=87, jd(2)=92, dobs(2)= -0.119,
  id(3)=120, jd(3)=125, dobs(3)= 0.811,
  id(4)=152, jd(4)=157, dobs(4)= 1.209,
  id(5)=184, jd(5)=189, dobs(5)= 0.538,
  id(6)=216, jd(6)=221, dobs(6)= 0.555,
  id(7)=260, jd(7)=262, dobs(7)= 0.464,
  id(8)=287, jd(8)=292, dobs(8)= -0.103,
  id(9)=320, jd(9)=325, dobs(9)= -0.367,
  id(10)=350, jd(10)=355, dobs(10)= -0.222,
  id(11)=445, jd(11)=450, dobs(11)= 0.771,
  id(12)=475, jd(12)=480, dobs(12)= -0.119,
  id(13)=508, jd(13)=513, dobs(13)= 0.811,
  id(14)=540, jd(14)=545, dobs(14)= 1.209,
  id(15)=572, jd(15)=577, dobs(15)= 0.538,
  id(16)=604, jd(16)=609, dobs(16)= 0.555,
  id(17)=648, jd(17)=650, dobs(17)= 0.464,
  id(18)=675, jd(18)=680, dobs(18)= -0.103,
  id(19)=708, jd(19)=713, dobs(19)= -0.367,
  id(20)=738, jd(20)=743, dobs(20)= -0.222,
 &end

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu