VMD-L Mailing List

From: Akshay Patny (akshay17_at_olemiss.edu)
Date: Sat Sep 16 2006 - 14:20:23 CDT

-----Original Message-----
From: Ilya Balabin [mailto:ilya_at_duke.edu]
Sent: Saturday, September 16, 2006 12:11 PM
To: Akshay Patny
Subject: Re: Membrane PlugIn issue

Hello Akshay,

> Q. I have realized that after embedding my GPCR in the POPC bilayer from
> VMD, some parts of the EC and IC loops remain outside the water slab.
> So, is there a way to increase the water slab of membrane a) either
> during membrane building or b) can it be done independently after a
> membrane has been built?

If I understand you correctly, you will be solvating the membrane-protein
complex at the next step - and that will surround the outlying protein
loops with water. After that, you will need to equilibrate that water with
protein and lipid heavy atoms coordinates fixed. That will take care of
restructuring water into solvation shells around the protein-membrane
complex, in the same way as for soluble proteins. The only reason I added
some water to the membrane is that water equilibration around the lipid
head groups is slow because of rather tight packing of the latter. For
protein parts, that should be less of a problem (again, cf. soluble
proteins), and equilibration of bulk water should be all you need.

Thanks for the note - I will keep it in mind when/if revising the
documentation to the membrane plugin. Please let me know if you have other
questions. Also, I would appreciate you posting this answer to the VMD
mailing list.

Best,
Ilya 

--
     Ilya Balabin, PhD                   Phone: (919) 660-1656
     P. M. Gross Chemical Laboratory     Fax:   (919) 684-4212
     Duke University                     Email: ilya.balabin_at_duke.edu
     Box 90349                           URL: http://www.chem.duke.edu/~ilya
     Durham, NC 27708-0349
"Research is what I'm doing when I don't know what I'm doing."