[gmx-users] Editing of the existing system

Mark Abraham Mark.Abraham at anu.edu.au
Fri Mar 30 15:34:34 CEST 2012

On 30/03/2012 5:27 PM, James Starlight wrote:
> Dear Gromacs Users!
> I have some system wich consist of protein in membrane-mimicking layer 
> surrounded by water. I want to modify my existing system by adding 
> small peptide fragment to this system. I want to dock this peptide to 
> the some part of my protein wich is situated  in the bottom water layer.
> While doing such task I've aligned both of the components of new 
> system in one desired dimmension so as the consequence I have 
> peptide.gro file in the desired orientation relative to my system.
> Now as I understood there are 2 possible ways
> 1- Manually copy_past peptide.gro into the system and run minimisation.
> 2- More accuracy- using genbox for such task
> genbox -cp Gs.gro -cs system.gro -o new.gro

I don't know that this works with a -cs file that is not all solvent.

> where Gs.gro is my peptide and system.gro is the system.
> But when I've tried such task I've obtain only peptide as well as some 
> solvent ( small part of water) as the consequence. How I could fix it 
> to obtain desired system with the removed overlapping water with the 
> new peptide ? What are the additions tips could you provide me about 
> such docking ?

Constructing a system is normally easiest if you remove all your 
solvent(s), paste in your interesting molecules somehow or other, and 
then rebuild the solvent with tools like genbox.


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