Closed farmaceut closed 2 months ago
Hi @farmaceut
In PyMOL, the dimension of the box is displayed in Å
npts 22 12 11
will generate a small box of
0.375 22 = 8.25 Å
0.375 12 = 4.5 Å
0.375 * 11 = 4.125 Å
where 0.375 Å is the spacing of the grid
Hi again @rwxayheee :) Thanks for quick response. So the solution would be either shifting spacing to 1 or change enpts following the equations
0.375 * X = 22
0.375 * Y = 12
0.375 * Z = 11
so npts 60 32 30
in that case?
Hi @farmaceut Yes npts 60 32 30
will give you the defined box in PyMOL without changing the spacing :>
@rwxayheee
Albeit, 4lxd.gpf
looks now like that:
npts 60 32 30 # num.grid points in xyz
gridfld 4lxd.maps.fld # grid_data_file
spacing 0.375 # spacing(A)
receptor_types A C NA OA N SA HD # receptor atom types
ligand_types A HD OA # ligand atom types
receptor 4lxd.pdbqt # macromolecule
gridcenter 21.3455 31.4093 8.11142 # xyz-coordinates or auto
smooth 0.5 # store minimum energy w/in rad(A)
map 4lxd.A.map # atom-specific affinity map
map 4lxd.HD.map # atom-specific affinity map
map 4lxd.OA.map # atom-specific affinity map
elecmap 4lxd.e.map # electrostatic potential map
dsolvmap 4lxd.d.map # desolvation potential map
dielectric -0.1465 # <0, AD4 distance-dep.diel;>0, constant
docking yielded same incorrect values:
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 1.048e+07 0 0
2 1.055e+07 2.02 3.311
3 1.073e+07 1.719 6.845
4 1.097e+07 1.944 2.312
5 1.1e+07 1.262 6.415
6 1.112e+07 2.075 6.526
7 1.123e+07 2.08 6.958
8 1.203e+07 1.709 2.266
9 1.208e+07 1.882 2.61
@farmaceut I got something like
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -4.222 0 0
Did you run autogrid4 with the new gpf file?
here's my output: output.pdbqt.txt
@rwxayheee
My issue! Forgot to run autogrid4
. Now it is more than good. Thank you!
'''
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
1 -4.208 0 0
2 -4.072 1.765 6.758
3 -3.961 1.832 2.393
4 -3.942 2.095 2.551
5 -3.857 2.16 6.683
6 -3.636 4.113 7.674
7 -3.548 2.621 3.775
8 -3.291 4.181 6.308
9 -3.019 3.248 7.181
'''
Hello,
I followed this tutorial to dock my new ligand into another protein. However, in the end, I obtained extremely high affinity values:
Here are the steps I followed:
1) I downloaded the 4lxd receptor from the PDB, removed everything except the protein, protonated it using Propka as implemented on the PDB2PQR webpage; then manually converted the resulting PQR format to PDB, and ran:
prepare_receptor -r 4lxd.pdb -o 4lxd.pdbqt
4lxd.pdb 4lxd.pdbqt
2) Then, I prepared the ligand (H4Fst) using:
mk_prepare_ligand.py -i H4Fst.mol -o H4Fst.pdbqt
H4Fst.mol H4Fst.pdbqt
3) I generated affinity maps for the AutoDock force field using:
pythonsh ./prepare_gpf.py -l H4Fst.pdbqt -r 4lxd.pdbqt -y
and obtained the 4lxd.gpf file, which I modified using Chimera visualization:I set
npts 22 12 11
andgridcenter 21.3455 31.4093 8.11142
leaving the remaining parameters as they were. 4lxd.gpf4) I ran AutoGrid4 using:
autogrid4 -p 4lxd.gpf -l 4lxd.glg
4lxd.glgand obtained all the maps enclosed in this file: maps.zip
5) Finally, I started Vina using the command:
vina --ligand H4Fst.pdbqt --maps 4lxd --scoring ad4 --exhaustiveness 32 --out output.pdbqt
and the output can be found here: output.pdbqt.txtAppreciate advice where I made the issue. Full_Archive.zip