VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 11 2017 - 03:13:10 CDT

Hi,
  I'm not sure what membrane plugin this is since you didn't say where
it came from, but it would be hard to give you any suggestions about
why it's giving you unexpected results without having the code. I think
that you should contact the author of the code directly and ask them
about this because they would undoubtlably know more than the people
on the mailing list who like me probably don't even know what code
you're using or where it came from.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 06, 2017 at 11:50:19AM +0530, Shashank Ranjan Srivastava wrote:
> Hi John,
>
> Membrane plugin is a tool that is use to calculate average thickness and
> thickness map throughout the trajectory. This tool is not available
> with VMD, we have to add this plugin externally in VMD plugin folder.
>
> So after adding this plugin you can see membrane analysis tool in
> extension-analysis of main vmd software, using that tool we can calculate
> thickness map by uploading trajectory file of your simulated molecule.
>
> My problem is by computing the thickness map it calculate the phosphate to
> phosphate distance of lipid molecule but in place of protein where no
> phosphate atom present it gives some number in that place also. Ideally it
> should not be there, mid region of map suppose to be white that is
> basically protein *(beta barrel)* position.
>
> Below I am attaching the thickness map image in form of contour plot where
> different colour represents different thickness at that place.
>
> How I can get white colour in place of protein.
>
> Thank you,
>
> On Thu, Apr 6, 2017 at 12:57 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> > Hi,
> > The only VMD "membrane" plugin I'm aware of in VMD is a tool for
> > building lipid membranes by replicating a template membrane box,
> > either POPC/POPE and generating a new structure. That tool doesn't
> > "calculate" anything, it only generates a structure. I'm afraid that
> > without substantially more detailed information about exactly what
> > steps you took and what your outcome was, that nobody would be able
> > to give you a solution to the problem you are having.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Wed, Apr 05, 2017 at 05:16:29PM +0530, Shashank Ranjan Srivastava wrote:
> > > Hello,
> > > I am trying to calculate membrane thickness using membrane plugin tool
> > > (version 1.1) but in place of protein it shows some random colour
> > that
> > > should not be there because I am specifically selecting P-atom that
> > is not
> > > there in protein.
> > > how to fix this problem? could you please help me out to fix this
> > problem.
> > > Thank You
> > > --
> > > Shashank Ranjan Srivastava
> > > Molecular Biophysics Laboratory
> > > Department of Biological Sciences,
> > > IISER-Bhopal,
> > > Madhya Pradesh
> >
> > --
> > 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/
> >
>
>
>
> --
> Shashank Ranjan Srivastava
> Molecular Biophysics Laboratory
> Department of Biological Sciences,
> IISER-Bhopal,
> Madhya Pradesh 

-- 
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/