Re: Lipid and protein interactions

From: snoze pa (snoze.pa_at_gmail.com)
Date: Mon Feb 22 2010 - 10:24:55 CST

Hi Marie, I agree with Alex. Please follow a nice tutorial at

http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm

I am sure this will help.

Goodluck

S

On Sat, Feb 20, 2010 at 9:49 AM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Fri, 2010-02-19 at 15:25 -0800, Marie N wrote:
>> Hey,
>
> marie,
>
>> 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?
> http://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/
>
>> 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.
>
> cheers,
>   axel.
>
>>
>> Thank you,
>>
>> Marie Nielsen
>>
>>
>
> --
> Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
> http://sites.google.com/site/akohlmey/
>
> Institute for Computational Molecular Science
> Temple University, Philadelphia PA, USA.
>
>

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