AMBER Archive (2009)

Subject: Re: [AMBER] building quadruplex with NAB

From: case (
Date: Tue Oct 27 2009 - 21:23:29 CDT

On Tue, Oct 27, 2009, Peter Varnai wrote:

> Currently, I use ideal G-tetrad _bases_ from a database pdb to get the
> distance bounds using 'useboundsfrom' for the core and then embed all
> coordinates with pembed. It gives acceptable final structures,
> however, when testing with rcsb's validation server, there are quite a
> few chirality problems around certain atoms.

This is a common-enough problem in distance geometry, since distances alone do
not determine chirality. As pointed out below, the distance-geometry part of
NAB has suffered from neglect, but it would be good to try to revive it.

> It would be nice if 'getchivol' and 'setchivol'
> could be applied automatically around each atom using a database,
> otherwise, inputting this for a larger molecule is not feasible.

The *.chi files in amber11/dat/reslib subdirectories were intended to do this.
What happened is that the molecule mechanics part of Amber (and NAB) diverged
from the reslib structures, and the latter are only partly functional.

> 3) I would like to try to build the quadruplex without using distance
> geometry as in in the examples/, however, I cannot
> even get this to run properly. Is it possible to run this example?
> for me it complains about 'setreskind: ERROR: unknown rkind H'. are right. The NAB code has evolved since the original examples
were created, but the examples didn't keep up with the changes in the
underlying code. I'll try to see what I can do here. For the moment, you
would have to use program_6 as inspiration for how you might build
tetraplexes, but not (unfortunately) as a truly working example.

I'm cc-ing this to Tom Macke: (Tom: do you have any time, or memory, to try to
reconstruct how the triplexes were originally built?)

Thanks for the report; sorry I can't get a simple fix.


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