VMD-L Mailing List

From: t.shivam_at_iitg.ernet.in
Date: Wed Apr 11 2018 - 04:01:52 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
>
>
Hello,
If you have downloaded the tutorial files for namd tutorial correctly the
topology file must be in "1-1 build" directory", the topology file should
be in your active directory, or else you have to type the path of the
directory containing topology file in your script, for psfgen to read it,

in case you still don't find it, here is the link

http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-files/1-1-build/top_all27_prot_lipid.inp

also there is a mailing list for tutorials also, in case you are interested

"http://www.ks.uiuc.edu/Training/Tutorials/mailing_list/"

also it will be convenient for others and you too if you write a subject
for your mail.

regards
shivam
>
>