AMBER Archive (2004)

Subject: AMBER: NMR constraint problem

From: Andrew Box (
Date: Tue Dec 07 2004 - 21:06:02 CST


I am trying to run minimization and molecular dynamics simulated annealing,
based off the DNA tutorial, but using a drug DNA complex (6 base pairs +
drug). If i run the simulation without an nmr restraint file (RST, file
attached) the run goes fine, but as soon as i add the restraint file i get
the following error in the *.out file (c3.min.ann.out, file attached)

Requested file redirections:
Restraints will be read from file: RST
Here are comments from the DISANG input file:
# 13 BEN HC 13 BEN H1 3.07

ERROR: r1 -> r4 (and r1a -> r4a) must be monotonically increasing; Offending
COM ( -1)-COM ( -1) NSTEP1= 0 NSTEP2=
R1 = 1.300 R2 = 1.800 R3 = 1.350 R4 = 1.850 RK2 = 20.000 RK3 =

But when i look at the restraint file, this is what it shows.

# 13 BEN HC 13 BEN H1 3.07
  ixpk= 0, nxpk= 0, iat= 397, 395, r1= 1.30, r2= 1.80, r3= 3.07, r4= 3.57,
      rk2=20.0, rk3=20.0, ir6=1, ialtd=0,

Somehow R3 and R4 are getting mixed up. Any idea on how to correct this
error, with out having to edit the entire restraint file. This happens
error occurs with whatever constraint is listed first in the RST file.

This is the command i am using:
sander -O -i -o c3.min.ann.out -c c.inpcrd -p c.prmtop -r
c3.restrt -x c.ann3.mdcrd

I am running Amber7 in RedHat Enterprise 3.

Thanks in advance.


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