VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Sep 16 2019 - 21:49:31 CDT

Evgenii,
  Can you send me a .tar.gz file containing the PDB file with the NaN
so that I can reproduce the crash locally? Although I don't expect VMD
to accept a NaN as a valid atomic coordinate, I really don't want to see
the program crashing in the way that happened for you, so I'd like to add
an extra safety check in the loading code to catch this earlier in the
loading process, and thereby prevent such crashes. If you can share the
structure file with me or at least show me an example of an problematic
atom record line from your file, that would be great.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Sep 17, 2019 at 01:59:47AM +0000, Kliuchnikov, Evgenii wrote:
> Hello,
> The problem was that one of the coordinates was nan, so VMD was not able
> to load this structure.
> Thank you for your response,
> Evgenii
>
> --------------------------------------------------------------------------
>
> Ot: John Stone <johns_at_ks.uiuc.edu>
> Otpravleno: 16 sentyabrya 2019 g. 21:07
> Komu: Kliuchnikov, Evgenii <Evgenii_Kliuchnikov_at_student.uml.edu>
> Kopiya: Miro Astore <miro.astore_at_gmail.com>; vmd-l_at_ks.uiuc.edu
> <vmd-l_at_ks.uiuc.edu>
> Tema: Re: vmd-l: VMD segmentation fault (core dumped)
>
> Hi,
> It looks to me like VMD might be crashing during bond determination.
> What program generated the DCD file you're loading? Are you certain that
> your coordinates are in the right units? Do you have an associated PSF
> file to go with the PDB? Why are you converting the DCD file into a PDB?
> There may be trouble in the conversion you've done there. What program
> generated the PDB?
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Sep 16, 2019 at 10:51:16PM +0000, Kliuchnikov, Evgenii wrote:
> > I guess there is no useful information, but
> > Info) VMD for LINUXAMD64, version 1.9.4a29 (February 25, 2019)
> > Info)
> [1]https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!vt9fxkjPvaI!Oc_si53Zmu_wMBkmr5spE19JixqlqZEuYTbxYwDomVNoEqyhrgaFeNZKZSm3jTk2XNihMrlQxBgHkYQ$
> > Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> > Info) Please include this reference in published work using VMD:
> > Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> > Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> > Info) -------------------------------------------------------------
> > Info) Multithreading available, 12 CPUs detected.
> > Info) CPU features: SSE2 AVX AVX2 FMA
> > Info) Free system memory: 19GB (60%)
> > Info) Creating CUDA device pool and initializing hardware...
> > Info) Detected 1 available CUDA accelerator:
> > Info) [0] GeForce GTX 1060 6GB 10 SM_6.1 1.84 GHz, 5.9GB RAM, KTO,
> AE2,
> > ZCP
> > Warning) Detected X11 'Composite' extension: if incorrect display
> occurs
> > Warning) try disabling this X server option. Most OpenGL drivers
> > Warning) disable stereoscopic display when 'Composite' is enabled.
> > Info) OpenGL renderer: GeForce GTX 1060 6GB/PCIe/SSE2
> > Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> > Info) Full GLSL rendering mode is available.
> > Info) Textures: 2-D (32768x32768), 3-D (16384x16384x16384),
> Multitexture
> > (4)
> > Info) Detected 1 available TachyonL/OptiX ray tracing accelerator
> > Info) Compiling 1 OptiX shaders on 1 target GPU...
> > Info) Dynamically loaded 3 plugins in directory:
> > Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> > Info) File loading in progress, please wait.
> > Info) Using plugin pdb for structure file last_frame.pdb
> > Info) Using plugin pdb for coordinates from file last_frame.pdb
> > Info) Determining bond structure from distance search ...
> > Segmentation fault (core dumped)
> >
> >
> --------------------------------------------------------------------------
> >
> > Ot: Miro Astore <miro.astore_at_gmail.com>
> > Otpravleno: 16 sentyabrya 2019 g. 18:44
> > Komu: Kliuchnikov, Evgenii <Evgenii_Kliuchnikov_at_student.uml.edu>
> > Kopiya: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
> > Tema: Re: vmd-l: VMD segmentation fault (core dumped)
> >
> > Hi, can you post the full error message?
> > On Tue, 17 Sep 2019 at 04:17, Kliuchnikov, Evgenii
> > <[1]Evgenii_Kliuchnikov_at_student.uml.edu> wrote:
> >
> > Hello VMD users,
> > I have pdb-file and dcd-trajectory that can be loaded into that
> pdb.
> > After that I save last frame of this trajectory, but when I try to
> load
> > this last frame in vmd it gives me segmentation fault error. What
> could
> > be the problem?
> > Sincerely,
> > Evgenii
> >
> > References
> >
> > Visible links
> > 1. [2]mailto:Evgenii_Kliuchnikov_at_student.uml.edu
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [3]https://urldefense.com/v3/__http://www.ks.uiuc.edu/*johns/__;fg!vt9fxkjPvaI!Oc_si53Zmu_wMBkmr5spE19JixqlqZEuYTbxYwDomVNoEqyhrgaFeNZKZSm3jTk2XNihMrlQTNCqY1k$
> Phone: 217-244-3349
> [4]https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!vt9fxkjPvaI!Oc_si53Zmu_wMBkmr5spE19JixqlqZEuYTbxYwDomVNoEqyhrgaFeNZKZSm3jTk2XNihMrlQxBgHkYQ$
>
> References
>
> Visible links
> 1. https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!vt9fxkjPvaI!Oc_si53Zmu_wMBkmr5spE19JixqlqZEuYTbxYwDomVNoEqyhrgaFeNZKZSm3jTk2XNihMrlQxBgHkYQ$
> 2. mailto:Evgenii_Kliuchnikov_at_student.uml.edu
> 3. https://urldefense.com/v3/__http://www.ks.uiuc.edu/*johns/__;fg!vt9fxkjPvaI!Oc_si53Zmu_wMBkmr5spE19JixqlqZEuYTbxYwDomVNoEqyhrgaFeNZKZSm3jTk2XNihMrlQTNCqY1k$
> 4. https://urldefense.com/v3/__http://www.ks.uiuc.edu/Research/vmd/__;!vt9fxkjPvaI!Oc_si53Zmu_wMBkmr5spE19JixqlqZEuYTbxYwDomVNoEqyhrgaFeNZKZSm3jTk2XNihMrlQxBgHkYQ$ 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/