peptide-energy-landscape-exploration

A detailed tutorial for exploring the energy landscape of peptides using GMIN/OPTIM/PATHSAMPLE programs interfaced with AMBER. Steps to obtain and further analyse the heat capacity as a function of temperature are also explained.

Overall workflow

flowchart LR                                                                   
    A("AMBER<br>- tleap<br> - sander<br> #9888; symmetrise topology file<br> - perm.allow file<br> #129488; check if symmetrised")
    -->                                                                        
    B("GMIN<br> - atomgroups for group rotation<br> - data file (basin hopping)<br> #128204; optimise data file parameters<br> - data file (BHPT)")
    -->                                                                        
    C("PATHSAMPLE<br> - addminxyz<br> - connectpairs<br> #10052; QCI on cold fusion<br> - disconnectivity graph<br> #11088; untrap")
    -->                                                                        
    D("Calculation<br> - frustration metric<br> #128293; heat capacity")       
    -->                                                                        
    E("Graphics<br> #127794; disconnectivity graphs<br> #9004; pymol ray tracing")

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flowchart TD                                                                   
g("<p style='text-align:left'>#9888; symmetrisation script used depends on the force field used</p><p style='text-align:left'> #129488; in case symmetrisation script is not available for a particular AMBER force field use existing script and check if it is working</p><p style='text-align:left'> #128204; arguments of sloppyconv, tightconv, step, temperature need to be optimised</p><p style='text-align:left'> #10052; use quasi-continuous interpolation when cold fusion is diagnosed</p><p style='text-align:left'> #11088; untrap parameters need to be fine tuned</p><p style='text-align:left'> #128293; local minima contributing to low temperature peak found using CvHSA program</p><p style='text-align:left'> #127794; Details about modifying linewidth, scalebar and colouring disconnectivity graphs</p><p style='text-align:left'> #9004; making figure using pymol script</p><p style='text-align:left'> ;</p>")

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1. Install AMBER
2. Clone softwarewales git repository
3. Compile executables for GMIN, OPTIM, and PATHSAMPLE
4. Create initial topology and coordinates files using AMBER
5. Create better starting geometry (coordinates file) using sander in AMBER
6. Symmetrise the topolgy file
7. Create perm.allow file for use with OPTIM and for checking symmetrisation
8. (Optional) Check if the symmetrisation script is working properly
9. Create an atomgroups file for use with GROUPROTATION keyword in GMIN
10. Obtain global minimum for monomer using basin-hopping
11. Optimise parameters in the data file for use with GMIN
12. Run basin-hopping parallel-tempering (BHPT) using optimised parameters
13. (Optional) Restore an existing basin-hopping parallel-tempering calculation
14. Add local minima obtained from GMIN into a PATHSAMPLE database using ADDMINXYZ keyword
15. Connect local minima to the global minimum using CONNECTPAIRS keyword in PATHSAMPLE
16. (If cold fusion diagnosed) Run CONNECTPAIRS with quasi-continuous interpolation (QCI)
17. Diagnose artificial frustration by plotting disconnectivity graphs
18. Fine tune parameters for UNTRAP that will then be used to remove artificial frustration
19. Run UNTRAP within PATHSAMPLE
20. Calculate frustration metric as a function of temperature
21. Calculate heat capacity as a function of temperature
22. Find local minima that contribute to low temperature peak in Cv and colour them on the disconnectivity graph
23. Extract coordinates of desired local minimum using EXTRACTMIN in PATHSAMPLE
24. Find energy decomposition for a local minimum
25. Ray trace structure of a peptide using Pymol
26. Miscellaneous