I want to insert the drug at a certain distance from the membrane. The membrane is prepared in Charmm-GUI.
1. Do I have to remove water and ions from the membrane, add the drug molecule with the gmx insert_molecules command, and then add water and ions again?
Because I tried without removing water and ions and used the replace flag. In the minimization stage, the complex became Irregular.
2. Should I make a restraint position file for the drug?
3. And the last question, does anyone have experience using the Charmm-GUI to insert the drug? it means that instead of the peptide or protein file, import the PDB file of the drug and insert it in a certain distance.
I would be happy to know your opinions and get your advice.
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