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 ? Thanks, JAmes
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