VMD-L Mailing List

From: Ramon Guixà (ramonguixxa_at_gmail.com)
Date: Tue Apr 11 2017 - 03:59:52 CDT

Hi Ranhan,

I guess the Membrane plugin you refer is MEMBPLUGIN, an external VMD
plugin. Please post your question to
https://sourceforge.net/p/membplugin/discussion/general/, we'll be glad to
help.

Best,
Ramon

On Tue, Apr 11, 2017 at 10:13 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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)Â 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/
>
>