[gmx-users] pdb2gmx illegal instruction

Mark Abraham Mark.Abraham at anu.edu.au
Tue Mar 21 06:55:13 CET 2006

Dongsheng Zhang wrote:
> Dear All,
> I want to run gromacs in supercomputer center at my school. When I used
> pdb2gmx, it gave me an error message as follows:
> illegal instruction (core dumped out)
> Could anyone give a clue what's happening? Thank you in advance.

We've got about as much chance of guessing what's wrong as your car 
mechanic has if you ring them up and say the car doesn't work :-)

You'll need to tell us more about what you're doing - what command, 
general nature of the input, etc.

Having said that, gromacs will only do the above when you are running 
code that tests for things like sse/sse2/3dnow hardware support without 
catching failure properly. I would not think that running pdb2gmx does 
such a test... however, if so, it suggests you are running an executable 
that wasn't compiled for your execution hardware.


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