VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Tue Apr 10 2018 - 18:51:32 CDT

Hi John,

On this page http://www.ks.uiuc.edu/Training/Tutorials/ there is a set of
files available for download necessary for running the NAMD tutorial.

>From a quick look at the folder 1-1-build the file you are missing is
present within that folder.

Hope this helps.

/A

On Apr 11, 2018 09:51, "JOHN FLANAGAN" <jmf27_at_psu.edu> wrote:

> 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
>
>
>
>