VMD-L Mailing List

From: Nikhil Maroli (scinikhil_at_gmail.com)
Date: Fri Sep 18 2015 - 02:42:58 CDT

Dear all,
im doing the tutorial when i enter the folowing code im facing these
problems ,please tell me what i should do now

thanks in advance

tutorials in this link (
http://www.ks.uiuc.edu/Training/Tutorials/namd-index.html)

compbio1_at_compbio1:~/namdT/1-1-build$ vmd -dispdev text -e ubq.pgn
Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
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, 8 CPUs detected.
Info) Free system memory: 13631MB (85%)
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.
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
1.6.2
too many arguments specified
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.
vmd > -dispdev text -e ubq.pgn
invalid command name "-dispdev"
vmd > exit
Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
Info) Exiting normally.
compbio1_at_compbio1:~/namdT/1-1-build$ vmd -dispdev text -e wat sphere.tcl
Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
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, 8 CPUs detected.
Info) Free system memory: 13640MB (85%)
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.
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
Info) File loading in progress, please wait.
ERROR) Unable to determine file type for file 'sphere.tcl'. Assuming pdb.
ERROR) Could not read file sphere.tcl
ERROR) Loading of startup molecule files aborted.
ERROR) Error opening file wat
ERROR) couldn't open "wat": no such file or directory
vmd > clear
[3;J
vmd > exit
Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
Info) Exiting normally.
compbio1_at_compbio1:~/namdT/1-1-build$ vmd -dispdev text -e ubq.pgn
Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
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, 8 CPUs detected.
Info) Free system memory: 13631MB (85%)
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.
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
1.6.2
too many arguments specified
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over.

MOLECULE MISSING! Use resetpsf to start over. 

-- 
Ragards,
Nikhil Maroli