[Debichem-devel] Bug#644397: gromacs: pdb2gmx, version 4.5.5, fails with 'Illegal instruction' on i686, 3.0.0.1-686-pae (testing)
groenedraeck
groenedraeck at gmail.com
Wed Oct 5 13:37:45 UTC 2011
Package: gromacs
Version: 4.5.5-1
Severity: important
It was found that the pdb2gmx (v4.5.5) from the GROMACS (gromacs v4.5.5-1) fails with an 'Illegal instruction' after the 'Making bonds...' operation (see below).
The bug was first noted in gromacs 4.5.4-2 (bug report not filed, prior versions of gromacs not tested at this workstation), and persists in the recent gromacs 4.5.5-1. In both cases the gromacs packages and all dependencies were installed through aptitude. Although reproducible on a virtual machine (see below), the bug first appeared on a physical computer, equipped with a single 1 GHz AMD Duron processor, 514340k RAM, md0 raid1 controlled by mdadm.
In order to help in locating the source of the problem, all gromacs packages and dependencies were purged from the system. Hereafter, fftw-3.3 was obtained, compiled from source and installed, followed by obtaining, compiling and installing gromacs-4.5.5 from source. The procedure completed according to instructions (c.f. www.gromacs.org - Installation Instructions) and without any errors. However, the pdb2gmx bug was found to be present here also.
On all occasions, the bug was found to be reproducible by following the lysozyme (pdb: 1AKI) GROMACS tutorial (located at http://goo.gl/dxzex). Briefly, the pdb file was obtained, crystal water molecules were removed (two methods have been tried: (i) manual removal of all HOH's in vi; (ii) automatically using CHIMERA), and the resulting 1AKI_waterless.pdb was processed by pdb2gmx using the following command:
$ pdb2gmx -f 1AKI_waterless.pdb -o 1AKI_processed.gro -water spce
This command was executed in a user homedir as well as in /tmp, furthermore the filenames have been varied (w/o underscore, short filename variants), and the '-water spce' directive has also been omitted.
In all cases, the pdb2gmx program starts normally and prompts the user for the force field. Only the following force fields have been tried, but both were found to result in the same illegal instruction:
- 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
- 1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
The program creates an empty topol.top file and returns to the prompt after displaying:
[..]
Linking CYS-76 SG-601 and CYS-94 SG-724...
Start terminus LYS-1: NH3+
End terminus LEU-129: COO-
Checking for duplicate atoms....
Now there are 129 residues with 1960 atoms
Making bonds...
Illegal instruction
$
I will try to attach the full output to the bugreport.
Furthermore, the bug was found to be reproducable on a virtualbox-ose installation of Debian GNU/Linux testing (Wheezy) i368 (clean install of base system, standard system utilities, gromacs packages and dependencies). In contrary, on an amd64 virtualbox installation of the base system, standard system utilities and gromacs plus all dependencies, the command completes normally without any error. Hence, the bug seems to be i368-specific.
In conclusion, this bug report concerns the pdb2gmx command of gromacs 4.5.5-1, which fails with an 'Illegal instruction' on i368/i686 architectures running Debian GNU/Linux testing (Wheezy) on both a physical computer (1 GHz AMD Duron) as well as on a virtualized vbox i386 installation.
-- System Information:
Debian Release: wheezy/sid
APT prefers testing
APT policy: (500, 'testing')
Architecture: i386 (i686)
Kernel: Linux 3.0.0-1-686-pae (SMP w/1 CPU core)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages gromacs depends on:
ii gromacs-data 4.5.5-1
ii libc6 2.13-21
ii libfftw3-3 3.2.2-1
ii libx11-6 2:1.4.4-2
ii libxml2 2.7.8.dfsg-4
Versions of packages gromacs recommends:
ii cpp 4:4.6.1-2
gromacs suggests no packages.
-- no debconf information
$ dpkg --status gromacs
Package: gromacs
Status: install ok installed
Priority: extra
Section: science
Installed-Size: 13384
Maintainer: Debichem Team <debichem-devel at lists.alioth.debian.org>
Architecture: i386
Version: 4.5.5-1
Depends: gromacs-data (= 4.5.5-1), libc6 (>= 2.7), libfftw3-3, libx11-6, libxml2 (>= 2.7.4)
Recommends: cpp
Breaks: radiance (<= 3R8+20070924.dfsg-1)
Description: Molecular dynamics simulator, with building and analysis tools
GROMACS is a versatile package to perform molecular dynamics, i.e. simulate
the Newtonian equations of motion for systems with hundreds to millions of
particles.
.
It is primarily designed for biochemical molecules like proteins and lipids
that have a lot of complicated bonded interactions, but since GROMACS is
extremely fast at calculating the nonbonded interactions (that usually
dominate simulations) many groups are also using it for research on non-
biological systems, e.g. polymers.
.
GROMACS offers entirely too many features for a brief description to do it
justice. A more complete listing is available at
<http://www.gromacs.org/content/view/12/176/>.
Homepage: http://www.gromacs.org/
-------------- next part --------------
$ pdb2gmx -f 1AKI_waterless.pdb -o 1AKI_processed.gro -water spce
:-) G R O M A C S (-:
Go Rough??????? Many An???????ese Seri???????rs
:-) VERSION 4.5.5 (-:
Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen,
Aldert van Buuren, P?r Bjelkmar, Rudi van Drunen, Anton Feenstra,
Gerrit Groenhof, Peter Kasson, Per Larsson, Pieter Meulenhoff,
Teemu Murtola, Szilard Pall, Sander Pronk, Roland Schulz,
Michael Shirts, Alfons Sijbers, Peter Tieleman,
Berk Hess, David van der Spoel, and Erik Lindahl.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2010, The GROMACS development team at
Uppsala University & The Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) pdb2gmx (-:
Option Filename Type Description
------------------------------------------------------------
-f 1AKI_waterless.pdb Input Structure file: gro g96 pdb tpr etc.
-o 1AKI_processed.gro Output Structure file: gro g96 pdb etc.
-p topol.top Output Topology file
-i posre.itp Output Include file for topology
-n clean.ndx Output, Opt. Index file
-q clean.pdb Output, Opt. Structure file: gro g96 pdb etc.
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-chainsep enum id_or_ter Condition in PDB files when a new chain should
-merge enum no Merge multiple chains into a single
-ff string select Force field, interactive by default. Use -h for
-water enum spce Water model to use: select, none, spc, spce,
-[no]inter bool no Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool no Interactive termini selection, instead of charged
-[no]lys bool no Interactive lysine selection, instead of charged
-[no]arg bool no Interactive arginine selection, instead of charged
-[no]asp bool no Interactive aspartic acid selection, instead of
-[no]glu bool no Interactive glutamic acid selection, instead of
-[no]gln bool no Interactive glutamine selection, instead of
-[no]his bool no Interactive histidine selection, instead of
-angle real -nan Minimum hydrogen-donor-acceptor angle for a
-dist real -nan Maximum donor-acceptor distance for a H-bond (nm)
-[no]una bool no Select aromatic rings with united CH atoms on
-[no]ignh bool no Ignore hydrogen atoms that are in the coordinate
-[no]missing bool no Continue when atoms are missing, dangerous
-[no]v bool no Be slightly more verbose in messages
-posrefc real -nan Force constant for position restraints
-vsite enum none Convert atoms to virtual sites: none, hydrogens
-[no]heavyh bool no Make hydrogen atoms heavy
-[no]deuterate bool no Change the mass of hydrogens to 2 amu
-[no]chargegrp bool yes Use charge groups in the .rtp file
-[no]cmap bool yes Use cmap torsions (if enabled in the .rtp file)
-[no]renum bool no Renumber the residues consecutively in the output
-[no]rtpres bool no Use .rtp entry names as residue names
Select the Force Field:
>From '/usr/share/gromacs/top':
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
8: CHARMM27 all-atom force field (with CMAP) - version 2.0
9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
15: [DEPRECATED] Encad all-atom force field, using full solvent charges
16: [DEPRECATED] Encad all-atom force field, using scaled-down vacuum charges
17: [DEPRECATED] Gromacs force field (see manual)
18: [DEPRECATED] Gromacs force field with hydrogens for NMR
14
Using the Oplsaa force field in directory oplsaa.ff
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading 1AKI_waterless.pdb...
WARNING: all CONECT records are ignored
Read 'LYSOZYME', 1001 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 129 residues with 1001 atoms
chain #res #atoms
1 'A' 129 1001
All occupancies are one
Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 1
Reading residue database... (oplsaa)
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 56
Sorting it all out...
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.1#
WARNING: unsupported proton mass multiplier (-nan) in pdb2top
Processing chain 1 'A' (1001 atoms, 129 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 213 donors and 184 acceptors were found.
There are 254 hydrogen bonds
Will use HISE for residue 15
Identified residue LYS1 as a starting terminus.
Identified residue LEU129 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS6 MET12 HIS15 CYS30 CYS64 CYS76 CYS80
SG48 SD87 NE2118 SG238 SG513 SG601 SG630
MET12 SD87 1.166
HIS15 NE2118 1.776 1.019
CYS30 SG238 1.406 1.054 2.069
CYS64 SG513 2.835 1.794 1.789 2.241
CYS76 SG601 2.704 1.551 1.468 2.116 0.765
CYS80 SG630 2.959 1.951 1.916 2.391 0.199 0.944
CYS94 SG724 2.550 1.407 1.382 1.975 0.665 0.202 0.855
MET105 SD799 1.827 0.911 1.683 0.888 1.849 1.461 2.036
CYS115 SG889 1.576 1.084 2.078 0.200 2.111 1.989 2.262
CYS127 SG981 0.197 1.072 1.721 1.313 2.799 2.622 2.934
CYS94 MET105 CYS115
SG724 SD799 SG889
MET105 SD799 1.381
CYS115 SG889 1.853 0.790
CYS127 SG981 2.475 1.686 1.483
Linking CYS-6 SG-48 and CYS-127 SG-981...
Linking CYS-30 SG-238 and CYS-115 SG-889...
Linking CYS-64 SG-513 and CYS-80 SG-630...
Linking CYS-76 SG-601 and CYS-94 SG-724...
Start terminus LYS-1: NH3+
End terminus LEU-129: COO-
Checking for duplicate atoms....
Now there are 129 residues with 1960 atoms
Making bonds...
Illegal instruction
$
-------------- next part --------------
processor : 0
vendor_id : AuthenticAMD
cpu family : 6
model : 7
model name : AMD Duron(tm) processor
stepping : 0
cpu MHz : 1001.722
cache size : 64 KB
fdiv_bug : no
hlt_bug : no
f00f_bug : no
coma_bug : no
fpu : yes
fpu_exception : yes
cpuid level : 1
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 sep mtrr pge mca cmov pat pse36 mmx fxsr sse syscall mmxext 3dnowext 3dnow up
bogomips : 2003.44
clflush size : 32
cache_alignment : 32
address sizes : 34 bits physical, 32 bits virtual
power management: ts
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