[gmx-users] packing lipids

[Shima Arasteh]

Thanks Peter.
:-)

 
Sincerely,
Shima


----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Monday, September 24, 2012 6:26 PM
Subject: Re: [gmx-users] packing lipids

What does trace show? (Trace is supposed to draw a vertex between each
alpha carbon). VMD has no knowledge of connectivity, it can only draw
bonds through distance calculatoin between consecutively numbered atoms.
Perhaps there is a misnumbering of the .gro file.

On 2012-09-24 07:48:17AM -0700, Shima Arasteh wrote:
> 
> 
>  In fact, the structure visualized by VMD and choosing line as draw style is ok, but the second structure of protein ( I mean the choosing ribbons) shows a broken structure. How come? what does it mean?
> 
> Thanks in advance.
> 
> 
> Sincerely,
> Shima
> 
> 
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc: 
> Sent: Monday, September 24, 2012 2:09 PM
> Subject: Re: [gmx-users] packing lipids
> 
> 
> 
> On 9/24/12 6:22 AM, Shima Arasteh wrote:
> >
> > Dear gmx users,
> >
> > Is it  possible that the protein got broken during shrinking iteration of packing lipids around the  protein?
> >
> 
> Only if it were broken to begin with.  This is a rather vague statement; if you 
> need further help, you will have to be a lot more specific about what's going on.
> 
> -Justin
> 
> -- 
> ========================================
> 
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
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==================================================================
Peter C. Lai            | University of Alabama-Birmingham
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