Re: [AMBER] Hairpin

From: Hugh Heldenbrand <>
Date: Tue, 14 Jun 2011 06:41:07 -0500


I have done this recently, so I thought I would reply. I would say that
this is not a "standard" feature of NAB, but with a little massaging and
luck you can make it happen. For me, the luck part was that there was a
NMR structure of a DNA hairpin that was similar in sequence to the DNA
hairpin that I wanted to simulate. Most importantly, the triloop of
residues that formed the bend in the DNA hairpin NMR structure was a GCA
triloop with a sheared G-A pair (PDB code 1ZHU), which is what I wanted
to simulate and which would have been very difficult to generate "by
hand" using NAB commands. Additionally, there was a single additional
Watson-Crick base pair in the NMR structure at a position that was
correct for the sequence I wanted to simulate.

With the triloop and single additional base pair in place, I was able to
delete the rest of the residues from the PDB that I did NOT want in my
sequence and use NAB commands to add in additional base pairs (some
Watson-Crick, some not) at the positions needed for the sequence I
wanted to simulate. This took a lot of trial and error and I spent a
lot of time getting the residues from the original PBD oriented so that
I could tack on a helix of my own additional residues. The final
structure which I generated still had a lot of stretched bonds and bad
contacts which required very careful minimization and low-temperature MD
to get to a structure near equilibrium. I only used NAB to generate a
PDB of the DNA hairpin that I wanted to simulate; I then used leap to
generate parameter and coordinate files for simulation in NAMD.

So, to answer your question, yes it is possible, but it's a lot easier
if you have at least a triloop structure to start with.

-Hugh Heldenbrand
Graduate Student, U of MN

On 06/14/2011 04:42 AM, Shesh Nath wrote:
> To
> Amber
> Sir,
> Is it possible to simulate dna hairpin using nab in Amber Tool
> 1.2.

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Received on Tue Jun 14 2011 - 05:00:10 PDT
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