Hi, i have a doubt regarding the charge of the molecule. my ligand have charge so i need to add ions to it . can you please tell me how to add ions like chlorine and sodium
Hii! I am facing a totally different problem, not related to this tutorial. So I have a docked complex, and after solvating when I am visualizing it in pymol or chimera or vmd, the unit cell boundaries are totally out of my solvated strucutre. Can you please help? Thank you :)
Hey! How to strip water from my prmtop and mdcrd file? I ran an MD simulation using Amber 20 and I just want to look at my peptide and therefore need to strip water. I tried using parmed but I get an error saying that the parmed command does not exsist. Can you help? Thank you!
To strip water from prmtop and mdcrd files, you have to use parmed and cpptraj respectively. If parmed is not opening then kindly check whether Amber20 is properly installed or not. Also, you can try to source the amber.sh file.
