Re: Lipid and protein interactions

From: Axel Kohlmeyer (
Date: Sat Feb 20 2010 - 09:49:08 CST

On Fri, 2010-02-19 at 15:25 -0800, Marie N wrote:
> Hey,


> I am a high school student doing some work relating to the lipid
> membranes and protein interactions.

you've earned my respect for taking on such a project.

unfortunately, from the description below, it is very
difficult to find out what you are trying to do, so i
suspect that nobody here will be able to help you unless
you provide some more details about what exactly you
did and where you are getting error messages.

> I am trying to use NAMD energy to find the interaction energies

does that mean you are trying to use the NAMD
energy plugin in VMD?

> between the lipid and the protein. However I am having trouble

what exactly is your test system? i would assume that you
have a lipid bilayer and an embedded protein. if yes, where
or how did you get this? if not, what are you looking at?

> getting the program to properly identify the two molecules. It says it
> can only identify one molecule. How do I fix this?

hmmm? a lipid bilayer would consist of many molecules.
otherwise you won't get any useful information.

where does "it" say you have only one molecule?
and what exactly is "it"?

assuming that you are indeed using VMD and the NAMD energy
plugin, then it looks as if you are getting confused
by the VMD nomenclature that calls a single _data set_ a
"molecule" (which is for historical reasons), which may
indeed contain many molecules. to use the NAMD energy plugin,
it is actually required to have everything in one "molecule"
or else the plugin won't work.

i hope this can help you at least a bit further.


> Thank you,
> Marie Nielsen

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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