From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Aug 01 2012 - 01:20:53 CDT
If you read the output file correctly, the psf and pdb are loaded without
problems. Than afterwards it tries to load another pdb file with an empty
path. Look to your script where else you try to use a pdb file. Check the
path as it seems namd cannot read the path to the file as it tells you file
‘’ not found.
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag
von Maria Antonieta Sanchez Farran
Gesendet: Dienstag, 31. Juli 2012 21:52
An: Aron Broom
Cc: Branko; namd-l
Betreff: Re: namd-l: NAMD 2.9: Segmentation fault?
Thanks Branko and Aron for your suggestions. I've tried before re-writing
the lines and using the "good" .conf from the other mutants, with no
success. I tried it once again and I still have the same memory error.
I will try Branko's suggestion of using VegaZZ to make sure the PDB file is
correct. Although the PDB file can be read by VMD.
Branko - I've run this simulation in a cluster and in my local machine, with
I will keep trying...
On 07/31/2012 03:14 PM, Aron Broom wrote:
Maybe try retyping the coordinate part of the file. That is, delete that
line entirely, and reenter it. I think it is something like Branko
suggested, some minor little problem with how things are being read that is
keeping it from finding your actual PDB file.
You said a bunch of mutants ran fine? Do the config files look the same?
Can you just take one of those mutant files, and change the location of the
file path manually to be this one that isn't working?
Essentially the error message is telling you that NAMD think you want it to
open nothing for the PDB, that is, it thinks " is the name of the PDB file
you entered after "coordinates". So it must be some very minor specific
On Tue, Jul 31, 2012 at 2:47 PM, María Antonieta Sánchez Farrán
Thanks Branko, my namd configuration files (and all my files are made in
linux). I am not sure what could be happening with the PDB.c code - for some
reason it doesn't read the file.
On 07/31/2012 02:42 PM, Branko wrote:
Did you made your namd configuration file in windows? End of lines
(different in linux and windows) from time to time can make problems. It is
likely that some lines in your configuration file cannot be read properly;
likely you check everything else and should be OK.
On 7/31/2012 8:14 PM, María Antonieta Sánchez Farrán wrote:
Yes, I have an ASCII pdb file. I can perfectly load the structures and I see
that there is no problem with it.
On 07/31/2012 02:02 PM, Branko wrote:
Do you have ASCII pdb file? If you have try to use this file without packing
(i.e. tgz, gz, or similar). System of ~ 35,000 is snot so big, so it is
reasonable to pack the files only for transfer from (for example) computer
to computer or similar. Can you load your PDB file to VMD (or GUI taht you
use), and check is everything is OK?
On 7/31/2012 7:44 PM, María Antonieta Sánchez Farrán wrote:
Dear NAMD Users,
I hope you can give me some insight on how to solve this issue. I have tried
running a simulation of a solvated protein (~35,000 atoms) using
NAMD_2.9_Linux-x86_64-ibverbs in a Red Hat Enterprise Linux Server release
5.8. It seems that it has problems reading the PDB file although the file
exists and the path is correct. I have generated the pdb and psf files with
psfgen and no errors appear. Other mutant of this protein runs perfectly,
and there is no difference in the original input file or method to generate
the pdb and psf files. I tried to run this in the NAMD 2.8 Multicore 64 bit
version and it also failed. I traced the error in the NAMD source files and
have found that it relates to the PDB.c code, the instance when opening a
PDB file. Please find below an extract of the log file from the simulation.
I also include the log message for different NAMD versions below. I have
checked NAMD Wiki Troubleshooting, and the archives in the mailing list but
I haven't been able to find how to sort this out. Any help would be much
In NAMD 2.9, this error appears:
Info: SUMMARY OF PARAMETERS:
Info: 180 BONDS
Info: 447 ANGLES
Info: 566 DIHEDRAL
Info: 46 IMPROPER
Info: 6 CROSSTERM
Info: 119 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 0.129473
Info: TIME FOR READING PDB FILE: 0.0585861
Command = zcat .Z
Filename.Z = .Z
Command = gzip -d -c .gz
Filename.gz = .gz
FATAL ERROR: Cannot open file '' for input in PDB::PDB.: No such file or
In NAMD 2.7 run on the same cluster, this error appears:
ob started on lionxh38.hpc.rcc.psu.edu at Mon Jul 30 20:03:43 EDT 2012
[lionxh38:11380] *** Process received signal ***
[lionxh38:11380] Signal: Segmentation fault (11)
[lionxh38:11380] Signal code: Address not mapped (1)
[lionxh38:11380] Failing at address: 0x14e8
[lionxh38:11380] [ 0] /lib64/libpthread.so.0 [0x32f0c0eb70]
[lionxh38:11380] [ 1]
[lionxh38:11380] [ 2] namd2(_ZN9ScriptTcl9initcheckEv+0x62) [0x82b842]
[lionxh38:11380] [ 3]
[lionxh38:11380] [ 4] namd2(TclInvokeStringCommand+0x91) [0x939c88]
[lionxh38:11380] [ 5] namd2 [0x96fad8]
[lionxh38:11380] [ 6] namd2(Tcl_EvalEx+0x176) [0x97011b]
[lionxh38:11380] [ 7] namd2(Tcl_EvalFile+0x134) [0x967b24]
[lionxh38:11380] [ 8] namd2(_ZN9ScriptTcl3runEPc+0x14) [0x82e244]
[lionxh38:11380] [ 9] namd2(_Z18after_backend_initiPPc+0x223) [0x4daf93]
[lionxh38:11380]  namd2(main+0x24) [0x4db074]
[lionxh38:11380]  /lib64/libc.so.6(__libc_start_main+0xf4)
[lionxh38:11380] *** End of error message ***
mpirun noticed that process rank 0 with PID 11380 on node
lionxh38.hpc.rcc.psu.edu exited on signal 11 (Segmentation fault).
I also tried running this in NAMD 2.8 multicore version (running Ubuntu
11.04) and I receive a memory overflow message. I include the output below.
*** buffer overflow detected ***:
======= Backtrace: =========
No virus found in this incoming message.
Checked by AVG - www.avg.com
Version: 9.0.930 / Virus Database: 2437.1.1/5167 - Release Date: 07/31/12
-- María Antonieta Sánchez Farrán Doctoral Candidate Department of Chemical Engineering The Pennsylvania State University No virus found in this incoming message. Checked by AVG - www.avg.com Version: 9.0.930 / Virus Database: 2437.1.1/5167 - Release Date: 07/31/12 09:25:00 -- María Antonieta Sánchez Farrán Doctoral Candidate Department of Chemical Engineering The Pennsylvania State University -- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo -- Maria Antonieta Sanchez Farran Doctoral Candidate Department of Chemical Engineering The Pennsylvania State University
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