AMBER Archive (2006)

Subject: RE: AMBER: faulty ambpdb compilation?

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Mar 16 2006 - 12:44:23 CST

Dear Benjamin,

Have you applied this bugfix?
http://amber.ch.ic.ac.uk/bugfixes/8.0/bugfix.29

All the best
Ross

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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Benjamin Juhl
> Sent: Thursday, March 16, 2006 10:16
> To: amber_at_scripps.edu
> Subject: AMBER: faulty ambpdb compilation?
>
> Dear Amber users,
>
> i am currently using amber8 compiled with a pathscale
> compiler. When i
> tried to construct pdb files from my restart files using ambpdb i got
> following error:
> -----------------------------------------------
> | New format PARM file being parsed.
> | Version = 1.000 Date = 03/16/06 Time = 17:58:37
>
>
> **** Segmentation fault! Fault address: 0x18
>
> Fault address is 4194280 bytes below the first valid
> mapping boundary, which is at 0x400000.
>
> This may have been caused by a struct access through a null pointer.
> Aborted
> -------------------------------------------------
>
> The strange thing is that i only get this for some of my
> restart files,
> while others can be used to create pdb files without error.
> When i tried
> to use those problematic restart files with an old ambpdb (from my
> amber7 installation), i could construct pdb files without
> generating an
> error.
> Has anyone experience with a similar problem?
>
> Thanks,
> Benjamin Juhl
> --------------------------------------------------------------
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