Modeling Training

Mock Modeling Training

Before you start Mock Modeling Training, you should spend few miniatures learning Unix Shell. If you want to learn more about programming, there are some lessons

Turn on Computer 3 in Rm 512 of Timken-Burnett Research Building, KCOM, ATSU. Open the MockModelingTraning folder. There are four subfolders in the MockModelingTraining folder. build3emlModel folder contains files to generate homology models; 3emlMd folder contains output files of molecular dynamic simulation; 3emlSa folder contains output files of simulated annealing simulation; charmm-gui folder contains tar file generated by CHARMM-GUI.

• To generate homology models.

  • Open build3emlModel folder, create a new folder and name it as taskDate (for example 3emlModelAug15). Copy all files in fileNeeded folder and paste them to your new folder.

  • Right click on blank inside your new folder, and click "open in Terminal".

  • Type following command and press enter.

  • python generateModels.py

  • 
    

  • It should generate 10 corrected_add_Out.B9999000#.pdb files and RMSD.txt file. Open RMSD.txt, the top one is the model with smallest RMSD. For example, the top one is "Out.B999005: 3.455954". Then you rename corrected_add_Out.B99990005 as bestModel5 (or whatever you can recognize).

• Align the best model you get with the template pdb file downloaded from OPM, built simulation system by CHARMM-GUI using the aligned model as input.

• To run a molecular dynamic simulation.

  • Run molecular dynamic simulation using Gromacs on Bridges.

  • Open 3emlMd folder, create a new folder and name it as taskDate (for example 3emlMdAug15).

  • Copy files in fileNeeded folder to your new folder. Right click on blank inside your new folder, and click "open in Terminal".

  • Get output files of molecular dynamics simulation from Bridges.

sftp jcai7@data.bridges.psc.edu

cd mdAnalysis

get processed.xtc
get step6.6_equilibration.mdp
get step7_production.tpr

• To run a simulated annealing simulation.

  • Run simulated annealing simulation on Bridges.

  • Open 3emlSa folder, create a new folder and name it as taskDate(for example 3emlSaAug16).

  • Copy files in fileNeeded folder to your new folder. Right click on blank inside your new folder, and click "open in Terminal".

  • Get output files of simulated annealing simulation from Bridges.

  • 
    

sftp jcai7@data.bridges.psc.edu

cd saAnalysis

get processed.xtc
get sa_protein.pdb
get step6.6_equilibration.mdp
get step7_production.tpr

• • Do RMSD analysis with the output files of simulated annealing simulation.

• Note: files have the same name in different places are different.