VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 28 2016 - 22:11:31 CST

Hi,
  Can you send me structure file and atom selection that you used
that caused the segmentation fault? If it occurs with both VMD 1.9.1
and 1.9.2, then you may have found something that isn't already fixed, so
the best thing would be to send me a copy of the files needed to reproduce
the problem.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 22, 2016 at 03:15:49AM +0000, yong zhou wrote:
> Dear John Stone
>
> Thanks for your quick reply.
> Actually, I have tried the binary version 1.9.2 for LINUX 64bit on a virtual machine with CentOS 7.
> The same error occurred.
> Therefore I do not know whether the compiled version of 1.9.2 will work or not.
>
> By the way, in installing vmd1.9.1, I installed the plugins at first, and then installed the src.
> How to install vmd1.9.2? The same as vmd1.9.1?
> Moreover, the version of tcl/tk on my computer is 8.6 and it seems that the version 8.5 is required.
> Does it matter in installing?
>
> Look forward to your reply.
>
> Best regards
>
> Yong Zhou
>
> ________________________________________
> From: John Stone <johns_at_ks.uiuc.edu>
> Sent: Thursday, January 21, 2016 3:34 PM
> To: yong zhou
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Running atomselect made a seg fault
>
> Hi,
> I would start out by using the newer VMD 1.9.2 version rather than 1.9.1,
> in case the cause of your problem has already been fixed. If you still
> experience the problem on VMD 1.9.2, then let me know and I will give you
> some suggestions to try that will help narrow down what may be occuring.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
>
> On Thu, Jan 21, 2016 at 03:11:24PM +0000, yong zhou wrote:
> > Hi,
> >
> > I have installed vmd1.9.1 on ubuntu14.
> >
> > Following the tutorial, I tried rmsd.tcl script in the tkconsole.
> >
> > However, a segmentation fault happened until the line of set frame0
> > [atomselect top "protein and backbone and noh" frame 0].
> >
> > According to the debugging, I found the error was from noh.
> >
> > Is there some idea for fixing this problem?
> >
> > Look forward to reply.
> >
> > Best regards
> >
> > Yong Zhou
>
> --
> 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
> http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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
http://www.ks.uiuc.edu/Research/vmd/