[gmx-users] packing lipids
shima_arasteh2001 at yahoo.com
Mon Sep 24 16:58:07 CEST 2012
----- 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.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
-- gmx-users mailing list gmx-users at gromacs.org
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
More information about the gromacs.org_gmx-users