[gmx-users] packing lipids
shima_arasteh2001 at yahoo.com
Mon Sep 24 17:05:20 CEST 2012
----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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.
> ----- 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>
> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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Peter C. Lai | University of Alabama-Birmingham
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