AMBER Archive (2006)

Subject: RE: AMBER: rmsd value for organic molecule

From: Varsha Goyal (vgusp_at_yahoo.ca)
Date: Mon Apr 24 2006 - 15:48:59 CDT

Dear Ross,

Thanks a lot.

Varsha Gupta

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:

> Dear Varsha,
>
> > trajin md1.mdcrd
> >...
> >
> > rms reference out rmsd_lowest_energy.dat @N,S,O
> time
> > 1.0
> >
> ---------------------------------------------------
> > after reading md21.mdcrd
> > i get following error
> > "Bus error"
>
> Bus error is a bit like a segfault it pretty much
> doesn't tell you much
> other than the code crashed. I doubt it is related
> to the atom types. More
> likely it is one of the following problems.
>
> 1) you select fit to reference but you don't read in
> a reference structure.
> You need a "reference filename" line before the rms
> line.
>
> 2) If the above (1) doesn't work try reducing the
> number of trajin's to 1
> and see if that works. You may be running out of
> memory trying to load all
> 21 trajectories in at once.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:-
> ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on
> request |
>
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