[gmx-users] packing lipids

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon Sep 24 16:58:07 CEST 2012

 Thanks Justin.


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, September 24, 2012 6:20 PM
Subject: Re: [gmx-users] packing lipids

On 9/24/12 10:48 AM, 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?

This is really more of a VMD question (there's a mailing list for that), but I'll take a shot anyway.  Broken ribbons sometimes result from other nearby atoms getting in the way.  That is, VMD detects "bonds" based simply on a distance search, and sometimes it guesses wrong or sometimes there's something legitimately wrong with your structure.  It could simply be that there is a lipid atom somewhat near a protein backbone atom and it is causing the rendering algorithm to fail.


-- ========================================

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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