AMBER Archive (2002)

Subject: Re: simulating dna

From: David A. Case (case_at_scripps.edu)
Date: Mon Nov 18 2002 - 18:29:22 CST

On Fri, Nov 15, 2002, Tod Pascal wrote:

> I was going through the tutorial on the website, attempting to simulate
> a holiday junction. After I solvate the molecule and add the
> counter-ions, I attempt to run a short minimization run to remove any
> potentially bad contacts (as described under the DNA tutorial as Step
> one). This work, however for the next step (Dynamics holding the solute
> fixed), it crashes and give me this error:
>
> vlimit exceeded for step 0; vmax = 60.1534683
>
> COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
> DEVIATION IS TOO LARGE
> NITER, NIT, LL, I AND J ARE : 0 0 1 27 28
>
> I'm following the tutorial as written, only using the holiday junction
> pdb file. What am I doing wrong?
>

looks like you still have bad initial forces; start with tempi=0 (if you
didn't do that already). If that still fails, you will probably have to
do more minimization before starting dynamics.

..good luck...dac 

-- 

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