Re: AMBER: Installation Problem, xleap can't load pdb files

From: Jonathan Neidigh <>
Date: Wed, 29 Oct 2003 07:54:18 -0800

I figured out the problem with loading pdb files (user error).
I am still curious if anyone has sucessfully installed mopac509mn on an SGI
using the current version of the MIPSpro compilers.


At 03:19 PM 10/28/2003 -0800, you wrote:
>I have compiled Amber7 with no problems. I used the Machine.sgi_mpi file
>provided with the Amber7 distribution (I also tried the Machine.sgi_mpi
>file on the SGI website). All of the tests except antechamber (problem
>with mopac) work fine (make test.leap, etc.). However, I get an error
>(Error: syntax error) in xleap whenever I try to load a pdb file, even the
>example tutorial files distributed with Amber. The same files seem to load
>fine in tleap. Is this a known bug? Any suggestions? I would like to use
>xleap if possible.
>Since I'm mentioning problems, I have also experienced a problem with
>mopac509mn. Compiling seems to work fine, but the test.timings file shows
>that tests 4, 6, 7, 8, 11, 13, and 14 failed (time: command terminated
>abnormally). If I run a single test file I get a Bus error (core dumped)
>error as shown here.
>protein 179# ../src/mopac509mn < test4.dat > test4.out
>Bus error (core dumped)
>Any suggestions? Details for my system are given below.
>Jonathan Neidigh
>Department of Biochemistry
>Loma Linda University
>Loma Linda, CA 92350
>Octane 2 running IRIX 6.5.18m
>2 400 MHz MIPS R12000(IP30) Processors with MIPS R12010 FPUs
>512 MB memory
>V6 graphics
>MIPSpro Compilers, version 7.4 (C++, C, f77, f90)

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Received on Wed Oct 29 2003 - 16:53:01 PST
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