[gmx-users] membrane protein tutorial

[Justin Lemkul]

On 11/15/13 10:04 AM, leila karami wrote:
> Dear Justin
>
> I am using your tutorial (membrane protein) for my system.
>
> I inserted my peptid into lipid bilayer. Now I want to solvate with
> water using genbox tool.
> To remove those water molecules are into lipid bilayer, I want to use
> keepbyz.pl script by Chris Neale. In step 4 of this script:
>
> 4. use vi to edit keepbyz.pl
>     - upperz and lowerz variables as you please
>     - sol to the name of your solvent molecule
>
> How to select upperz and lowerz? Based on what criterion?

These values specify the upper and lower bounds of the hydrophobic region of the 
membrane, i.e. the space between which you do not want any water.

> If I want to have z vector = 9 nm after solvation, which value of
> upperz and lowerz are appropriate?
>

Define the box and everything within it with editconf and decide from there.

> If I use another way, only reduction of the value of C from
> 0.15 to 0.375 in vdwradii.dat file is enough?
>

It is "enough" in most general cases, but it's not foolproof.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================