Reply To: Modeling phosphate ion binding site in protein.

[Anonymous]

Hi,
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/LigandBaseProtocol.cc line: 272

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

-nstruct 500

-out
-file
-renumber_pdb
-packing
-no_optH
-ex1
-ex1aro
-ex2
-docking
-randomize2
-uniform_trans 5
-ligand
-start_from 0.000 0.000 0.000 (as I want rosetta to search for binding site, like in case of blind docking)
-minimize_ligand

-mute core.util.prof ## dont show timing info
-mute core.io.database

Pls help …