AMBER Archive (2004)

Subject: FW: AMBER: Segmentation fault (core dumped) error of antechamber program

From: S. Frank Yan (SYan_at_gnf.org)
Date: Mon Jan 26 2004 - 12:12:39 CST


-----Original Message-----
From: S. Frank Yan
Sent: Friday, January 23, 2004 11:57 AM
To: amber_at_scripps.edu
Subject: RE: AMBER: Segmentation fault (core dumped) error of
antechamber program

The compiler is gcc version 3.2.3 20030502, and I used the
Machine.g77_mpich for compilation. The OS is Red Hat Linux Enterprise
WS 3.2.3-24. I didn't have mopac installed yet, and couldn't run the
test suite. Nonetheless, for conversion purpose the antechamber program
doesn't require a charge model. Also it happens to all the pdb files I
tested, all of which seem to be OK when visualized. Thanks, Frank

-----Original Message-----
From: David A. Case [mailto:case_at_scripps.edu]
Sent: Thu 1/22/2004 5:21 PM
To: amber_at_scripps.edu
Cc:
Subject: Re: AMBER: Segmentation fault (core dumped) error of
antechamber program
On Thu, Jan 22, 2004, S. Frank Yan wrote:
>
> I was trying to use the antechamber program to convert a .pdb file to
.ac
> file. The conversion was successful; however, I got a "Segmentation
fault"
> error every time. It's like:
>
> antechamber -fi pdb -i temp.pdb -fo ac -o temp.ac
> Segmentation fault (core dumped)
>

(a) What compiler, machine, operating system?

(b) Does your installation pass the antechamber test suite?

    cd $AMBERHOME/test
    make test.antechamber

(c) when you say "every time", do you mean that you have used different
pdb files? Or that it crashes repeatedly with the same input? If the
results
seem to depend on what pdb file you use, you will probably need to post
your "temp.pdb" file.

..regards...dac

-- 

================================================================== David A. Case | e-mail: case_at_scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

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