Dear Scientists
I want to make system for protein ligand complex for simulation study on Gromacs 4.5.6. I follow Justin tutorial ( http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html ). I got ligand topology from Prodrg server and added as per instruction given in tutorial. And also added ligand coordinates (found from Prodrg) at the end of protein.gro file to make complex.gro.
Problem: After editconf, when I open newbox_complex.gro file there is no ligand coordinates. I have no idea How to fix it? I tried many times.
Any suggestion or question for making problem more clear.
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