AMBER Archive (2006)

Subject: RE: AMBER: rmsd value for organic molecule

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Apr 24 2006 - 14:25:23 CDT

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

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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