AMBER Archive (2002)

Subject: Re: DNA structure get distorted

From: David Case (case_at_scripps.edu)
Date: Fri Apr 12 2002 - 11:27:10 CDT

On Thu, Apr 11, 2002, Monica wrote:

> I am running Simulated Annealing on DNA hexamer.My input
> file is:
> ----------------------------------------------------------------------------
> simulated annealing protocol, 63.5 ps
>
> &cntrl
> imin=0, ntx=1, nstlim=63500,
> temp0=100.0, tempi=100.0, igb=3
> ntt=1, ntb=0, ntf=1, nmropt=1, vlimit=20,
> ntpr=1000, ntt=1, ntwx=2544, ntwv=2544, ntwe=2544,
> cut=10.0, scee=1.2,
> &end
> #
> #Simple simulated annealing algorithm:

...rather non-simple annealing algorithm follows....

> but finally when I view structure it is distorted.

It is not possible to provide a very useful answer from just the complaint
"the structure is disordered...." without knowing what your restraints are,
how distorted it really is, etc. But you might think about the following:

(1) If you heat DNA up to 1000 degrees or more, and don't have *lots* of
stringent constraints, it will almost certainly not anneal back down to
a non-distorted structure. (Of course, this may not apply to you if your
constraints are very detailed.)

(2) Try much simpler runs: just run at 300K with your constraints: what
happens? Just heat to 500K, then cool back down, etc. It is unlikely
that there is a generic answer to your question that anyone on the list
will know...you need to experiemnt to see how your system behaves.

...good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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