From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Tue Jul 31 2012 - 13:04:59 CDT
Maria,
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 not 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?
Branko
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 appreciated.
>
> Thanks,
> Maria Antonieta
>
> 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
> Info:
> 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 directory
>
> 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]
> namd2(_ZN9NamdState14configListInitEP10ConfigList+0x779) [0x7e16b9]
> [lionxh38:11380] [ 2] namd2(_ZN9ScriptTcl9initcheckEv+0x62) [0x82b842]
> [lionxh38:11380] [ 3]
> namd2(_ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x28) [0x82de88]
> [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] [10] namd2(main+0x24) [0x4db074]
> [lionxh38:11380] [11] /lib64/libc.so.6(__libc_start_main+0xf4)
> [0x32f001d994]
> [lionxh38:11380] [12]
> namd2(_ZNSt19basic_ostringstreamIcSt11char_traitsIcESaIcEED1Ev+0x89)
> [0x4d7919]
> [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 ***:
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2 terminated
> ======= Backtrace: =========
> /lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7f0923291db7]
> /lib/x86_64-linux-gnu/libc.so.6(+0xfdcd0)[0x7f0923290cd0]
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(_ZN8Molecule23build_constraint_paramsEP10StringListS1_S1_P3PDBPc+0x332)[0x90b442]
>
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(_ZN9NamdState14configListInitEP10ConfigList+0x184a)[0x92302a]
>
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(_ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x84)[0x98a2a4]
>
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(TclInvokeStringCommand+0x88)[0xaa93e8]
>
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2[0xaac007]
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2[0xaad422]
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(Tcl_EvalEx+0x16)[0xaadc46]
>
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(Tcl_FSEvalFileEx+0x151)[0xb0fdf1]
>
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(Tcl_EvalFile+0x2e)[0xb0ffae]
>
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(_ZN9ScriptTcl4loadEPc+0x1a)[0x98ac7a]
>
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(_Z18after_backend_initiPPc+0x23a)[0x5019ea]
>
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2(main+0x22)[0x501d32]
>
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xff)[0x7f09231b1eff]
> /home/masf/source/NAMD_2.8_Source/Linux-x86_64-g++/namd2[0x4fc8a9]
>
>
>
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