AMBER Archive (2009)

Subject: Re: [AMBER] Segmentation fault in antechamber

From: albert albert (albertassonke_at_googlemail.com)
Date: Tue Nov 17 2009 - 11:04:46 CST

Thanks for all.

The pdb is linked.

Warm regards

Albert

On Mon, Nov 16, 2009 at 6:48 PM, Mark Williamson <mjw_at_sdsc.edu> wrote:

> albert albert wrote:
>
>> 1- cpc.pdb is a phycocyanin pdb download from RCSB.
>> 2- There is no output
>> 3- If I remove "-c bcc"; I receive the same error.
>> 4- I upgrade my system ubuntu 9.4 to 9.10, the compiler is gfortran.
>>
>> Thanks
>>
>
> If the program is segfaulting, it can be useful to recompile and rerun it
> in special manner to glean more information as to why it crashed. On a
> recent thread, I gave some instructions on how to do this. You should follow
> the points 1 to 3 at http://archive.ambermd.org/200911/0072.html , and
> then at step 4, run antechamber in a similar manner to which parmchk was run
> in gdb. This should hopefully provide more useful output to go on.
>
> Remember, you may need to install gdb if it is not already installed, and,
> if you're using Ubuntu, the following command should work:
>
> sudo apt-get install gdb
>
> Also, have you got the correct four letter code for the PDB file that you
> refer to or perhaps a link to it?
>
> regards,
>
>
>
> --
> Mark Williamson, Post Doc
> Walker Molecular Dynamics Group
> Room 395E
> San Diego Supercomputer Center
> 9500 Gilman Drive
> La Jolla, CA 92093-0505
> Email: mjw at sdsc.edu
> Office: 858-246-0827
>
>
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>



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