Re: AMBER: coordinates ******

From: David A. Case <>
Date: Thu, 25 Jan 2007 12:08:52 -0800

On Tue, Jan 23, 2007, kepa koldo burusco wrote:
> I'm running ptraj and carnal calculations over a
> trajectory file: RMSD, Radius of Gyration,
> Diffusion... using AMBER 7.
> The original calculation is a NPT Molecular Dynamics
> in CHCL3 solvent and box is a truncated octahedron (by
> the way, I am not removing the solvent molecules).
> My problem is that restart file (the reference
> structure) for RMSD calculations shows a few lines
> like the next ones:
> -59.4669830-843.8849945 568.4678259
> -61.0471413-843.3087710 567.9562990
> -59.1762415-845.5550610 568.0020731
> -59.1694863-843.5231680 570.1622704
> 23.1586695************ 614.6020183
> 22.5738716************ 615.3055373

Unfortunately, there is not much you can do to fix the restart file. You may
still be able to analyze the trajectory file, since it handles overflow
somewhat more gracefully, (although I don't know if that was true in Amber 7
or not....)

How long was the simulation? If you are getting very rapid diffusion on short
time scales (say a few nanoseconds) it might an indication that something is

More recent versions of Amber handle this problem in a better way (although
still not completely satisfactorily....)

...good luck..dac

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Received on Sun Jan 28 2007 - 06:07:24 PST
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