[gmx-users] Editing of the existing system

James Starlight jmsstarlight at gmail.com
Fri Mar 30 08:27:41 CEST 2012

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

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 ?


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