AMBER Archive (2006)

Subject: Re: AMBER: Sander NOE violations

From: Andrew Box (
Date: Thu Jul 06 2006 - 20:32:21 CDT

The restraint file was created by making a 7 column restraint file, then
converting it with make_dist command. Here is a few lines of the file:

  13 BEN Q31 8 THY H4' 3.40
  13 BEN Q31 9 GUA H1' 4.24
  13 BEN Q31 9 GUA H3' 4.44
  13 BEN Q31 9 GUA H4' 3.00
  13 BEN Q31 9 GUA Q5' 3.06
  13 BEN Q31 9 GUA Q5' 4.54
  13 BEN H15 10 CYT H1' 4.31
  13 BEN H161 13 BEN H9 3.75

The file was then added to a trotion angle restraint file and run with the
dynamics run.

Andrew Box
La Trobe University

>From: "David A. Case" <>
>Subject: Re: AMBER: Sander NOE violations
>Date: Thu, 6 Jul 2006 18:01:19 -0700
>On Thu, Jul 06, 2006, Andrew Box wrote:
> >
> > I am running nmr restraints during my dynamics runs in sander. When I
> > for the NOE violations in the out put file generated, I notice I have
> > violations between atoms that have no constraints placed on them.
>You don't say how the restraint file was created...Are you sure that there
>are no distance restrints between (say) C24-BEN-13 and C25-BEN-13?
>the only thing that should be printed here are pairs of atoms that are in
>distance restraint file. This is why I am asking if you are sure that no
>such restraints were present.
> > a small part of my out put file:
> >
> > First atom Last atom curr. value target deviation penalty
> >
> > C24 BEN 13 -- C25 BEN 13: 1.500 1.800 0.300 1.799 d
> > 0: 0
> > C24 BEN 13 -- *O3 BEN 13: 5.992 4.600 1.392 22.845 d
> > 0: 0
> >
> > In the first line, it denotes a problem between two carbon atoms that
> > connected with in aromatic ring. The second line shows a violation
> > between a carbon and oxygen atom that are separated by more than 8
> > bonds and have no NOE constraint between them.
> > Also, I have no idea what
> > the * in front of the atoms names mean, as I have used no * in any atom
> > names.
> >
>A "*" in front of an atom name means that that atom was part of a "group"
>of atoms (see the igr1 and igr2 variables). The atom name printed is the
>atom of the group, and the "*" is a signal that it is member of a group.
>hope is that knowing the last atom of the group will be enough to identify
>which group it is.
>Overall, it sounds like sander is not interpreting your RST file in the way
>you intended. If you set pencut to a negative value, and run (say) a
>single-point caclulation, you can see all of the restraints that are being
>applied, in the order that they appear in the RST file. You can examine
>each one, and try to figure out what is going on.
>..good luck...dac
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