6DDF-Fentanyl

Goal: MD simulation of mu opioid receptor (6DDF) with fentanyl bound in the orthosteric binding site.

Step 1: Fentanyl structure was extracted from 5TZO. This structure was edited with Maestro and saved as a mol2 file (FNT.mol2). During this process, correct double bonds were added to the benzene rings and +1 charge was added to N09. CHARMM general force field parameters (FNT.str) were generated using the CGenFF website (Username: Norimatsu, Frog504+512). These parameters were replaced by parameters developed by the Bondar group (FNT-Lesnik.prm, FNT-Lesnik.rtf).

Step 2: The MD system for 6DDF was built by CHARMM-GUI (see the screenshots) with custom-made topology and parameter file for fentanyl (which was manually placed in 6DDF).

Step 3: The PSC Bridges was used for minimization and equilibration of the system and for the final production run. The sbatch command was used with minimization.slu, equilibration.slu and production.slu.