AMBER Archive (2008)

Subject: Re: AMBER: double strand DNA break up (imaging)

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Thu Apr 24 2008 - 14:43:36 CDT

First off, search the AMBER e-mail reflector. "dna imaging" pops up a
number of hits, including:

        http://amber.ch.ic.ac.uk/archive/200707/0374.html

> During my simulation my DNA approaches the edge of the box and I get one
> strand on one side of the box and the other strand on the other side. I am
> using NAMD for the simulations and generating .dcd files ( "wrapAll" is
> "on"). When I reimage the trajectory using ptraj I still get the
> displacement of the two strands. Is there anything I can do about this? My
> ptraj script looks like this:
>
> trajin ../output/prod1-5ns.dcd
> trajin ../output2/prod5-10ns.dcd
> trajout prod1-10ns.dcd
> center :1-23
> image :1-23 bymask :1-23
> strip :WAT

What you want to do is center one of the strands, then image; this in
general works except in extremely small boxes or peculiar situations. If
you have a 12-mer DNA,

center :1-12 mass origin
image origin center
center :1-24 mass origin
image origin center familiar

Now if the DNA is rather bent or the box is rather small, this can
sometimes lead to the situation that the strands are still separated
(easily noticable by a large instantaneous jump in the RMSd).

To get around the pathological cases, you have to be a bit more tricky and
try not imaging around the center of mass (as above) but of a single
residue...

center :1 mass origin
image origin center
center :1-24 mass origin
image origin center familiar

No need to use the bymask option to image; you probably want to image all
molecules.

If this continues to be a problem you can either (1) hack the prmtop/PSF
to put the DNA strands into a single molecule (so they will always be
imaged together), or (2) hack up ptraj to be "smarter" regarding the
imaging; I've tended to do (1) as (2) has proven more difficult (less
general).

-- tec3
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