AMBER Archive (2004)

Subject: Re: AMBER: NMR constraint problem

From: John Bushnell (bushnell_at_ultra.chem.ucsb.edu)
Date: Wed Dec 08 2004 - 14:39:32 CST

Just a guess here, but when I've used a restraint file, the iat array
is terminated with a "0" (zero) like so:

   iat = 397, 395, 0, r1 = 1.30, ...

Perhaps it is confused when it reaches r1 while still reading iat[]?
Still, I don't see how it would end up with the values you see...

        - John

On Wed, 8 Dec 2004, Andrew Box wrote:

> Hi
>
> 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)
>
> RESTRAINTS:
> Requested file redirections:
> LISTOUT = POUT
> DISANG = RST
> 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
> restraint:
> ******
> COM ( -1)-COM ( -1) NSTEP1= 0 NSTEP2=
> 0
> R1 = 1.300 R2 = 1.800 R3 = 1.350 R4 = 1.850 RK2 = 20.000 RK3 =
> 20.000
>
> But when i look at the restraint file, this is what it shows.
>
> #
> # 13 BEN HC 13 BEN H1 3.07
> &rst
> 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,
> &end
>
> 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 anneal.in -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.
>
> AB
>
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