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.
Mark
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