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

From: Jonathan Neidigh <>
Date: Tue, 28 Oct 2003 15:19:59 -0800

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 Tue Oct 28 2003 - 23:53:01 PST
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