From: Subbusinger N (subbu813_at_gmail.com)
Date: Thu Dec 05 2013 - 06:02:32 CST

Hi,
This is Subrahmanyam,Research scholar, IIT Kharagpur. While uploading the
dcd file to genrate rmsd file I got the following message of killing the
dcd file.. This dcd file contains nearly 3400 frames. I tried on 32 bit it
didn't work. It suggested me to use 64bit which gave me the following
message while uploading. I tried to load dcd file by combining two dcdfiles
of 1000 and 2400. kindly any of suggest how to proceed.

Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
Info) http://www.ks.uiuc.edu/Research/vmd/

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, 4 CPUs detected.
Info) Free system memory: 4826MB (82%)
Warning) Detected a mismatch between CUDA runtime and GPU driver
Warning) Check to make sure that GPU drivers are up to date.
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: Mesa DRI Intel(R) Sandybridge Mobile
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (8192x8192), 3-D (256x256x256), Multitexture (8)
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
vmd > Info) Using plugin pdb for structure file
/home/pad/Desktop/2PS1_wb.pdb
Info) Using plugin pdb for coordinates from file
/home/pad/Desktop/2PS1_wb.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 440466
Info) Bonds: 296063
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 144914
Info) Waters: 144460
Info) Segments: 29
Info) Fragments: 144468 Protein: 2 Nucleic: 0
Info) Finished with coordinate file /home/pad/Desktop/2PS1_wb.pdb.
psfplugin) Detected a Charmm31 PSF file
Info) Using plugin psf for structure file /home/pad/Desktop/2PS1_wb.psf
Info) Analyzing structure ...
Info) Atoms: 440466
Info) Bonds: 296054
Info) Angles: 157384 Dihedrals: 18824 Impropers: 1136 Cross-terms: 444
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 144914
Info) Waters: 144460
Info) Segments: 29
Info) Fragments: 144468 Protein: 2 Nucleic: 0
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info) Using plugin dcd for coordinates from file
/home/pad/Desktop/t2PS1_wb_eq.dcd
Killed

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