VMD-L Mailing List

From: JOHN FLANAGAN (jmf27_at_psu.edu)
Date: Tue Apr 10 2018 - 16:36:48 CDT

Hi
  New to this so I downloaded NAMD,
VDM and the toppar from
UMaryland. Working through the ubiquitin example I hit a road
block. I have tried the toppar directory and in the vmd directory to no
avail. I looked in the directory and there is no .inp file of that name
just a .rtf file. Not sure how to proceed or where I went
wrong.

Cheers and thanks
John

1aon.pdb 1rc2.pdb
distance.tcl
toppar ubqp.pdb
1fqy.pdb 1ubq.pdb equilibration.dcd toppar_c31b1.tar.gz vmd-1.9.4a12
1j4n.pdb beta.tcl pulling.dcd ubiquitin.psf
1lda.pdb Chimera spinach_aqp.fasta ubq.pgn
johnf_at_Var2CSA:~/Downloads$ vmd -dispdev text -e ubq.pgn
/usr/local/lib/vmd/vmd_LINUXAMD64:
 /usr/lib/nvidia-390/libGL.so.1: no version information available
(required by /usr/local/lib/vmd/vmd_LINUXAMD64)
Info) VMD for LINUXAMD64, version 1.9.4a12 (December 21, 2017)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this refer!
 ence 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, 24 CPUs detected.
Info) CPU features: SSE2 AVX AVX2 FMA
Info) Free system memory: 61GB (97%)
Info) Creating CUDA device pool and initializing hardware...
Info) Detected 1 available CUDA accelerator:
Info) [0] Quadro K4000 4 SM_3.0 0.81 GHz, 2.9GB RAM, KTO, AE1, ZCP
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
1.7
ERROR: Unable to open topology file top_all27_prot_li!
 pid.inp

MOLECULE DESTROYED BY FATAL ERROR! Use re!
 setpsf 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 >

John M. Flanagan PhD.
Professor
Department of Biochemistry and Molecular Biology
Penn St. College of Medicine
Milton Hershey Medical Center
Hershey PA, 17033