AMBER Archive (2006)

Subject: Re: AMBER: coordinate out of bounds

From: j j (fantvamp_at_gmail.com)
Date: Thu Dec 14 2006 - 04:21:50 CST

Maybe if you have several MDCRD files for your MD,
you can do:
wc MDCRD_1, ...MDCRD_n; tail MDCRD_(n-1) MDCRD_n
or if you have only one:
tail MDCRD,
if there is not an EOF(EOL) in the last then
echo "\n" >> MDCRD(last or uniq),
suppossing you work under any unix-like kernel able to understand
the commands.
or if there is any extra line you can try removing them (do cp 1 1.bk)
before
processing you traj with ptraj.
JJ

2006/12/14, Miguel Ferreira <tetrass_at_hotmail.com>:
>
> Hi
>
> I want to do an ED calculation and used the following script
>
> trajin mds_500ps.mdcrd
> rms first @CA
> matrix covar name mcovar @CA out mcovar.dat
> analyse matrix mcovar out evec.pev vecs 25
> go
>
> The calculation takes about 2 minutes and I obtain the output files.
> However
> I also obtain the following error:
>
> ERROR in readAmberTrajectory(): Set #2501 has coordinate out of bounds (
> i.e.
> *****'s)
>
>
> [3] Done ptraj monomer.top < eigenvectors.in >
> eigenvectors.out
>
>
> I donīt understand this because my trajectory has only 2500 frames. Does
> anyone know what this error means?
>
>
> Thanks
> Miguel
>
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