VMD-L Mailing List
From: Peter Freddolino (petefred_at_umich.edu)
Date: Thu Oct 20 2016 - 21:38:02 CDT
This is a pool of dummy atoms used by molefacture in structure building. For molecules being acted upon in molefacture, you should only trust the molefacture panel itself, not the atom counts in the vmd main window.
> On Oct 20, 2016, at 3:30 PM, Raviteja Kurapati <tsii.ravi_at_gmail.com> wrote:
> But I am not clear about why 300 atom file loading when i start molefacture without making selection. Following startup message is coming when i open VMD:
> 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, 4 CPUs detected.
> Info) Free system memory: 13680MB (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.
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this X server option. Most OpenGL drivers
> Warning) disable stereoscopic display when 'Composite' is enabled.
> Info) OpenGL renderer: Gallium 0.4 on NV117
> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFS)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (512x512x512), Multitexture (8)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> vmd >
> I am working Fedora 23, Interl Xenon(R) processor, Graphics NV117 Gallium 0.4
> On Thu, Oct 20, 2016 at 11:59 PM, Raviteja Kurapati <tsii.ravi_at_gmail.com> wrote:
> Thank you Peter and John for your response. I have not given any selection. It is worked when i entered selection. Actually I want to insert my protein in mixed solvents. Is there any option or plugin available for VMD by which i can build initial configuration?
> Best Regards,
> Raviteja Kurapati
> On Thu, Oct 20, 2016 at 11:12 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
> Can you post the startup messages that VMD prints when you run it?
> What hardware and OS are you running on?
> John Stone
> On Thu, Oct 20, 2016 at 05:57:34PM +0530, Raviteja Kurapati wrote:
> > Hi, I am using vmd 1.9.2. No CUDA devices. When I open molfacture plugin,
> > atoms are not listed in molfacture window and OpenGL Display not showing
> > any atoms. But main window is showing a .xbgf file. What is the problem
> > and How can I solve this?
> > Best Regards.
> > Raviteja Kurapati
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349