To begin, open the Visual Dynamics or VD webpage and click on login to access the system login screen. After logging in, the simulation submission area, tutorials, and usage statistics can be accessed. For APO enzymes simulation submission, click on new simulation in the sidebar and click on the button APO.
Upload the free protein 4mgv. pdb file and select the AMBER94 Force field. Select the TIP3P water model, followed by the Cubic box.
Select 0.5 nanometer distance between the protein and the box edge. Check the option run in our servers to execute the simulation. Using UCSF Chimera, open the protein ligand complex 4mgv.
pdv, click residue, and set the code to D5I. Then under file, click save PDB, select save selected atoms only, set the file name to ligand. pdb, and click save.
Go to the Bio2Byte ACPYPE server and submit the generated ligand. pdb file from the output files. Click on new simulation, followed by protein ligand.
Upload the free protein 4mgv. pdb file and select the ligand files prepared in ACPYPE followed by MBER94 Force Field. Select the TIP3P water model followed by the Cubic box, and select 0.5 nanometer distance between protein and box edge.
Check the option run in our servers to execute the simulation. Click on my simulations in the sidebar, and then on download MDP files to download the simulation configuration files used. Click commands to download the list of commands executed by the platform, and click GROMACS Log to download the LOG file containing GMX command outputs.
Click results to download files generated by the GMX commands, and finally, click figure graphics to download graphs for analyzing each simulation step in image and XVG format to the computer. The protein backbone exhibited a root mean square deviation of less than 2.5 angstroms, and the radius of duration showed that the protein maintained its compactness in X, Y, and Z coordinates during the five nanosecond simulation. The average fluctuation distance of each amino acid in the protein structure, as shown by root mean square fluctuation, remained consistent throughout the five nanosecond simulation.
The system stabilized with a maximum force of less than 1000 kilojoules per mol per nanometer during the energy minimization process.
