From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Sep 15 2006 - 19:46:30 CDT

1-2) You will likely find that 5-10 A is not sufficient. I would
suggest perhaps more like 15 A on each side, since once you remove
the lipids overlapping with the protein and simulate, it will
shrink. That number of 4-5 lipids between the protein and the
boundary (meaning probably 10 lipids total between protein images) is
probably a good estimate to help you gauge how well your system is
built once you are done.

3) Once you have built your protein/membrane system and combined them
into a unified psf/pdb, use the solvate plugin to add an appropriate
amount of water afterwards.

http://www.ks.uiuc.edu/Research/vmd/plugins/solvate/

Let us know if this works for you!

On Sep 15, 2006, at 12:07 PM, Akshay Patny wrote:

> Hi
>
>
>
> As suggested by Dr. Ting, I am generating a POPC bilayer in VMD.
>
>
>
> As I mentioned, my GPCR protein is 320 residues in size and
> following are the XYZ dimensions
>
>
>
> Z ~ 67 A
>
> X ~ 54 A
>
> Y ~ 50 A
>
>
>
> 1. In the VMD, we can only define the X and Y dimensions of the
> POPC bilayer, so will it be fine if I go for something like X/Y =
> 60 or 65, so that I can appropriately center my GPCR protein in the
> bilayer?
>
>
>
> 2. A reference for Dr. Harel Weinstein says “studies have shown the
> appropriate distance between the solute protein and a simulation
> box boundary to correspond to ~4 to 5 layers of lipid
> molecules” [Lipid Bilayer used in the study was POPC bilayer] The
> AAPS Journal 2006; 7 (4) E871-E884. Would that be taken care of by
> building a bilayer with X/Y dimensions of 5-10 A greater than the X/
> Y dimensions of protein?
>
>
>
> 3. 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?
>
>
>
> I would appreciate any suggestions.
>
>
>
> Thanks and Kind Regards
>
> Akshay
>
>
>
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On
> Behalf Of Ting Wang
> Sent: Thursday, September 14, 2006 5:28 PM
> To: akshay17_at_olemiss.edu; vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: DPPC Bilayer Size
>
>
>
> Hi Akshay,
>
>
>
> VMD can not generate DPPC bilayer. Peter Tieleman's coordinates are
> fine but you will probably later have problems of embedding your
> protein into the membrane. A easier way is to generate POPC bilayer
> in VMD and use VMD scripts to do later on jobs. I have 118 POPC
> lipids for my GPCR protein.
>
>
>
> Ting
>
> ----- Original Message -----
>
> From: Akshay Patny
>
> To: vmd-l_at_ks.uiuc.edu
>
> Sent: Thursday, September 14, 2006 11:49 AM
>
> Subject: vmd-l: DPPC Bilayer Size
>
>
>
> Hi All
>
>
>
> I am trying to simulate a GPCR protein belonging to the rhodopsin
> family with amino acid length of 320 residues. Also, I would be
> using the pre-hydrated DPPC bilayer, can somebody suggest that for
> a GPCR protein of roughly 320 aa, how big DPPC bilayer would be
> appropriate to use e.g. 128 DPPC bilayer is available from Peter
> Tieleman’s website http://moose.bio.ucalgary.ca/index.php?page=Main .
>
>
>
> Also, can VMD ‘membrane’ van generate DPPC bilayer?
>
>
>
> Thanks
>
> Akshay Patny
>
> Graduate Research Assistant
> Faser Hall 417, Department of Medicinal Chemistry
>
> Research Institute of Pharmaceutical Sciences
> University of Mississippi
> University, MS 38677
> E-mail: akshay17_at_olemiss.edu
> Tel: 662-915-1286 (office); Web: www.olemiss.edu
>
>
>
>