Member Site Forums Rosetta 3 Rosetta 3 – General Modeling phosphate ion binding site in protein. Reply To: Modeling phosphate ion binding site in protein.


    As you said for croos docking experiment.. I have started doing that but I am having some problems as its new for me..
    1) As per the tutorial , I have created a parameter file for my phosphate ion using molfile_to_paramfile.
    2) Next, I prepared the receptor for docking by suing the lingand_rpkmin command . Here after generating the 10 structures how can I select the best one for further docking ..
    3) Okay say I ahev selected one structure , the next step is to provide the native structure.. I have it for my protein but phosphate ion is present in the crystal structure. So in this case shall I provide the native structure without phosphate ion one or not ??..
    4) Finally, coming to actual docking how to give the number of steps the dockign should continue … and how large should this number be in mycase ?

    After running the docking command I am getting the following errors :-

    ERROR: Pose has no jumps!
    ERROR:: Exit from: src/protocols/ligand_docking/ line: 272

    Here is the list of parameters that I used :-
    -rng mt19937
    -s 1GFL_mutate2_native_0002.pdb

    -nstruct 500

    -uniform_trans 5
    -start_from 0.000 0.000 0.000 (as I want rosetta to search for binding site, like in case of blind docking)

    -mute ## dont show timing info

    Pls help …