Re: AMBER: faulty ambpdb compilation?

From: Benjamin Juhl <>
Date: Thu, 16 Mar 2006 19:51:47 +0100

I had the bugfix.all (
applied which i got 22.feb 2006. I checked that file and it contained
the bugfix.29.

Benjamin Juhl

Ross Walker schrieb

>Dear Benjamin,
>Have you applied this bugfix?
>All the best
>|\oss Walker
>| HPC Consultant and Staff Scientist |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- |
>| | PGP Key available on request |
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>>-----Original Message-----
>>[] On Behalf Of Benjamin Juhl
>>Sent: Thursday, March 16, 2006 10:16
>>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.
>>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
>>Has anyone experience with a similar problem?
>>Benjamin Juhl
>>The AMBER Mail Reflector
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Received on Sun Mar 19 2006 - 06:10:22 PST
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