AMBER Archive (2009)

Subject: Re: [AMBER] Segmentation fault in antechamber

From: Mark Williamson (mjw_at_sdsc.edu)
Date: Mon Nov 16 2009 - 11:48:32 CST

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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