Frequently Asked Questions

  • Do I need to prepare my reference structure files?


    • Yes, you need to prepare reference structures of a protein and ligand:

    • Extract protein/ligand lines from the PDB file
    • Protein: grep ATOM 1yer.pdb > prot.pdb
    • Ligand:grep HET 1yer.pdb > tmp.pdb; grep -v HOH tmp.pdb > lig.pdb

    You can find more information on this page.

  • What do the output plots mean?


    • When clicking on the View Analysis button you are shown a RMSD plot and a cluster representative plot. The RMSD plot describes the average distance between atoms of superimposed structures. Orange shows a larger distance and therefore difference in structures. This means the binding pocket is more transient. The cluster representative plot shows the data that was clustered together to provide these results.


    The JSmol output shown when TRAPP Pocket Analysis is carried out, shows the differences found in binding pockets.

  • What do all of the parameters mean?


    • You can use the default settings which will allow results to be shown. However you can adjust the parameters to your needs. A small description of the parameters is shown if you hover the mouse over the input boxes.
    More information about the parameters can be found on this page.


  • Are there any limitations to this webserver?


    • Yes, the maximum number of snapshots in an input trajectory is limited to 5000 snapshots and the maximum file size is 500MB.
    More information can be found on this page.


  • Has the webserver been tested?


    • The webserver has been internally tested on multiple browsers.There are also 3 example applications on the webserver which can be found on this page.


  • Who do I contact if I would like to get more information or give feedback?


    • You can send an email to mcmsoft(at)h-its.org


  • The visualization of TRAPP analysis shows less snapshots than i have generated/uploaded?


    • Due to memory restrictions on the client computer, not all grids and snapshots can be visualized. If there are more than 100 snapshots in a trajectory to be used for pocket simulations - all snapshots will be taken into account in pocket property computations, but not all snapshots will be shown in Jsmol visualization ( the stride is calculated as: int(total_number_of_snapshots)/100 +1 ).


  • Why is TRAPP crashing during structure analysis?


    • We have observed that structure analysis for large systems (with over about 45000 atoms) crashes with a segmentation fault due to limitations for using openBabel to read structures.