AMBER Archive (2008)

Subject: Re: AMBER: Simulating DNA Backbone in NAB

From: David A. Case (case_at_scripps.edu)
Date: Wed Apr 02 2008 - 15:24:25 CDT

On Tue, Apr 01, 2008, Adelene Sim wrote:

> Hi, I'll like to do a MD simulation of just the DNA backbone (i.e. no
> side-chains, replace the bases by a H) in NAB. Is it possible to just add in
> entries into the force-field library (e.g. all_nucleic94.lib), where I
> remove the side chain atoms and replace them by a H atom? (Of course I'll
> also change the charges on the atom.)

The easiest way is probably to load the native nucleotides into xleap, then
visually remove the parts you don't want, and use the "saveoff" command to
create libraries. You might want to give your backbone-only residue a unique
name, so that it won't get confused with with regular names.

If you want to, you can try to just edit the lib files themselves, but that is
much trickier.

...good luck...dac
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