Comments (6)
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
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Hi @farmaceut Yes npts 60 32 30
will give you the defined box in PyMOL without changing the spacing :>
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@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
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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?
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@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
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@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
'''
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Related Issues (20)
- Details on scoring function terms HOT 3
- Autogrid4 Atom Type Error with Large Ligand Database HOT 6
- An internal error occurred in ../../../src/lib/parse_pdbqt.cpp(69). HOT 3
- Autogrid4 raise error "dyld: Library not loaded:" HOT 8
- Weird protein split in flexible docking HOT 7
- Is AutoDock-Vina applicable to peptides? HOT 3
- Docking to zinc atoms in a non-3,1 tetrahedral conformation HOT 4
- Vina flexible docking HOT 4
- PyPi suggests windwos compatibility of python bindings.
- rdkit.six not found HOT 1
- Problems with Binary installation HOT 1
- Autogrid4 Unknown receptor type: HOT 1
- Vina runtime error: The ligand is outside the grid box HOT 1
- I am getting this error while doing flexible autodock docking HOT 1
- H-bond term HOT 2
- Flexible docking tutorial : no HD map file after autogrid4 HOT 1
- Differences between `*_rigid.pdbqt` and `*.pdbqt` files of receptors HOT 2
- Issue : An internal error occurred in ../../../src/lib/tree.h(101) HOT 3
- Problem in generation of some map files during flexible autodock docking. HOT 3
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