AMBER Archive (2006)

Subject: Re: AMBER: RE: Respgen segemtation fault

From: Simon Whitehead (
Date: Thu Apr 20 2006 - 07:30:48 CDT

Dear Prof. Case,

After running gcc -v i got the following information;

Reading specs from /usr/local/lib/gcc-lib/i686-pc-linux-gnu/3.3.5/specs
Configured with: ../configure --disable-shared --enable-languages=c,c++,f77 --enable-version-specific-runtime-libs
Thread model: posix
gcc version 3.3.5

uname -a gave the following info;

Linux 2.6.11-1.1369_FC4 #1 Thu Jun 2 22:55:56 EDT 2005 i686 i686 i386 GNU/Linux

I`m still quite inexperienced with linux so please could you tell me what i need to do to run a debugger?

Many thanks


-----Original Message-----
From: on behalf of David A. Case
Sent: Thu 4/20/2006 12:49 PM
Subject: Re: AMBER: RE: Respgen segemtation fault
On Wed, Apr 19, 2006, Simon Whitehead wrote:

> Thanks for your reply Prof. Case. I tried what you suggested but that also
> ended in a segmentation fault. However, i didn`t have the file in my
> $AMBERHOME/test/antechamber/tp directory, only a pdb file, so converted it
> using antechamber. Is this ok because this is what i have been doing with my
> input files? I have also listed below a copy of the .ac file i am using as
> the input for respgen, maybe this might provide some insight? The c
> compilers i have used are gcc and g++. Does this give you any more clues?

What does "uname -a" say (what type of computer do you have) and "gcc
--version" (which version of gcc)?

Your input, and all inputs I have tried, work fine for me; so there must be
something different about your system and mine, and we need to try to figure
out what it is. You may have to fire up a debugger at your end to find out
where the segfault is coming from.

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