Reply To: -dock_pert problem

[Anonymous]

Re: the use of “TER” card: in one of my latest runs I used the ppked file directly which didn’t have the TER line between the docking partners (FAC and BD). I used the flag -partners FAC_BD. this run was ok as far as I can tell, that is, it was able to find the docking partners properly without the correct TER line formatting. The question is is it necessary to use the TER line between the docking partners or is it enough just to use the flag. I used to add the TER line between the docking partners and also use the flag but it seems now the TER line may not be neessary??

(part of the pdb file I use for the run is below:

ATOM 2047 3HD1 LEU F 183 -4.727 51.468 50.201 1.00 0.00
ATOM 2048 1HD2 LEU F 183 -3.723 51.486 53.114 1.00 0.00
ATOM 2049 2HD2 LEU F 183 -5.368 51.013 52.623 1.00 0.00
ATOM 2050 3HD2 LEU F 183 -4.369 49.896 53.583 1.00 0.00
ATOM 2051 N ARG A 58 8.567 60.239 53.307 1.00 0.00
ATOM 2052 CA ARG A 58 8.457 61.689 52.936 1.00 0.00
ATOM 2053 C ARG A 58 8.204 62.580 54.153 1.00 0.00

…….
ATOM 4098 1HD2 LEU A 183 13.225 67.944 53.114 1.00 0.00
ATOM 4099 2HD2 LEU A 183 14.457 66.756 52.623 1.00 0.00
ATOM 4100 3HD2 LEU A 183 14.925 68.179 53.583 1.00 0.00
ATOM 4101 N ARG C 58 -0.501 74.210 53.307 1.00 0.00
ATOM 4102 CA ARG C 58 -1.701 73.391 52.936 1.00 0.00
ATOM 4103 C ARG C 58 -2.346 72.726 54.153 1.00 0.00
………
ATOM 6148 1HD2 LEU C 183 -9.502 74.392 53.114 1.00 0.00
ATOM 6149 2HD2 LEU C 183 -9.089 76.053 52.623 1.00 0.00
ATOM 6150 3HD2 LEU C 183 -10.556 75.747 53.583 1.00 0.00
ATOM 6151 N GLU B 1 -28.704 17.452 68.716 1.00 0.00
ATOM 6152 CA GLU B 1 -27.344 17.691 69.205 1.00 0.00
ATOM 6153 C GLU B 1 -26.698 18.717 68.302 1.00 0.00

……….
ATOM 7766 1HB SER B 121 3.824 9.133 56.018 1.00 0.00
ATOM 7767 2HB SER B 121 3.120 8.501 54.512 1.00 0.00
ATOM 7768 HG SER B 121 4.680 7.093 55.423 1.00 0.00
ATOM 7769 N ASP D 1 3.590 34.214 71.207 1.00 0.00
ATOM 7770 CA ASP D 1 2.674 33.242 71.806 1.00 0.00
ATOM 7771 C ASP D 1 2.893 33.246 73.296 1.00 0.00

………
ATOM 9407 2HH1 ARG D 108 -8.681 -2.507 83.250 1.00 0.00
ATOM 9408 1HH2 ARG D 108 -5.513 -1.411 84.297 1.00 0.00
ATOM 9409 2HH2 ARG D 108 -6.397 -2.307 83.077 1.00 0.00
TER
# All scores below are weighted scores, not raw scores.
#BEGIN_POSE_ENERGIES_TABLE ox40-edited_0001

……….

Cheers.

Thank you for looking into this smlewis. As an added note, which may or may not be relevant: I was able to run -docking_local_refine successfully before trying -dock_pert. However, when I first attempted -docking_local_refine, I did get some errors about “foldtree” which seemed to indicate it was having issues figuring out which protein was receptor/ligand. As far as I could gather, my input structures were formatted correctly with a “TER” line separating chains ABCD from EF. This error was resolved when I added the -docking_partners flag.

Thanks again. Please do let me know if you hear back anything…