an aptamer and a lot of stupid problems

From: Xxxxxxxx Xxxxxxx (
Date: Mon Feb 11 2008 - 23:09:38 CST


I'm just a stupid newbie and wanted to check out VMD and NAMD.
What I actually wanted to do is to simulate the secondary structure of
an aptamer (exactly a 73 bases single stranded DNA).
My first problem was to generate a pdb-file for my ssDNA. what I did
(please don't laugh), I generated a pdb of a DNA double helix, opened
it in an editor and deleted the whole B chain, as I couldnt find a
tool for generating single stranded DNAs.
So I have a helical ssDNA - a really instable thing.
As the DNA is a very long unfolded molecule, it needed a huge waterbox
around (using 5A of water around) my resulting psf has about 200.000

My big problem is, using a modified version of the namd tutorial
equilibration, that my computer is too tiny.
as I'm just a student of biochemistry and want to check out the
software, i just use a PC (with 2 processor cores, 2 GB memory) and I
don't have a cluster at home.

During equilibration I always got the error "grid becomes too small".
When I refine the Grid, I get the error "are we out of memory?". So
the equilibration doesnt work cause either my grid or my memory breaks

What can I do? It is just a DNA with 73 bases, there should be a way
to make it work.

Thanks for any suggestions


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