Open Yuwei-Pan opened 2 months ago
rwxayheee
commented
2 months ago Hi @Yuwei-Pan
Can you kindly share your input files (ligand PDBQT, map FLD, GPF, and DPF, if you use them) and hardware information? It seems like gpu_gradient_minAD couldn't minimize the next generations at some step, but I'm not sure about the exact cause. Having the input files would be tremendously useful for others to reproduce this issue
atillack
commented
2 months ago @Yuwei-Pan Which version of AD-GPU are you using and what GPU are you running on?
atillack
commented
2 months ago @Yuwei-Pan Also, one thing to try is to run the AD-GPU OpenCL version using make DEVICE=OCLGPU NUMWI=128 OVERLAP=ON. While Cuda and OpenCL should be functionally similar there may be some slight differences.
Yuwei-Pan
commented
2 months ago Hi @Yuwei-Pan Can you kindly share your input files (ligand PDBQT, map FLD, GPF, and DPF, if you use them) and hardware information? It seems like
gpu_gradient_minADcouldn't minimize the next generations at some step, but I'm not sure about the exact cause. Having the input files would be tremendously useful for others to reproduce this issue
The ligand PDBQT:
REMARK Name = .\14207ds.pdb
REMARK 9 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: _1 and _11
REMARK 2 A between atoms: _1 and _20
REMARK 3 A between atoms: _4 and _24
REMARK 4 A between atoms: _6 and _14
REMARK 5 A between atoms: _8 and _15
REMARK 6 A between atoms: _8 and _25
REMARK 7 A between atoms: _12 and _24
REMARK 8 A between atoms: _13 and _16
REMARK 9 A between atoms: _17 and _29
REMARK x y z vdW Elec q Type
REMARK _______ _______ _______ _____ _____ ______ ____
ROOT
ATOM 3 C UNL 1 10.266 2.510 7.756 0.00 0.00 +0.085 A
ATOM 4 C UNL 1 11.600 2.927 7.779 0.00 0.00 +0.179 A
ATOM 7 C UNL 1 11.995 4.026 7.001 0.00 0.00 +0.188 A
ATOM 10 C UNL 1 11.026 4.686 6.230 0.00 0.00 +0.138 A
ATOM 11 N UNL 1 9.744 4.280 6.192 0.00 0.00 -0.233 NA
ATOM 18 CA UNL 1 9.395 3.224 6.919 0.00 0.00 +0.165 A
ENDROOT
BRANCH 10 12
ATOM 12 C UNL 1 11.370 5.825 5.378 0.00 0.00 +0.131 A
ATOM 13 C UNL 1 12.537 6.484 5.191 0.00 0.00 +0.227 A
ATOM 14 O UNL 1 12.329 7.458 4.240 0.00 0.00 -0.447 OA
ATOM 15 C UNL 1 11.027 7.346 3.891 0.00 0.00 +0.193 A
ATOM 16 C UNL 1 10.500 8.266 2.857 0.00 0.00 +0.109 C
ATOM 17 N UNL 1 10.407 6.399 4.526 0.00 0.00 -0.212 NA
ENDBRANCH 10 12
BRANCH 3 1
ATOM 1 S UNL 1 9.699 1.088 8.651 0.00 0.00 -0.123 S
ATOM 2 C UNL 1 8.858 1.887 10.053 0.00 0.00 +0.090 C
ENDBRANCH 3 1
BRANCH 4 5
ATOM 5 O UNL 1 12.592 2.263 8.443 0.00 0.00 -0.490 OA
ATOM 6 C UNL 1 12.679 2.468 9.833 0.00 0.00 +0.277 C
ENDBRANCH 4 5
BRANCH 7 8
ATOM 8 O UNL 1 13.268 4.468 6.969 0.00 0.00 -0.502 OA
ATOM 9 H UNL 1 13.836 3.910 7.238 0.00 0.00 +0.292 HD
ENDBRANCH 7 8
BRANCH 18 19
ATOM 19 C UNL 1 7.939 2.838 6.769 0.00 0.00 +0.357 C
ATOM 20 OXT UNL 1 7.102 3.184 7.583 0.00 0.00 -0.243 OA
BRANCH 19 21
ATOM 21 O UNL 1 7.705 2.162 5.679 0.00 0.00 -0.476 OA
ATOM 22 H UNL 1 6.845 2.035 5.590 0.00 0.00 +0.295 HD
ENDBRANCH 19 21
ENDBRANCH 18 19
TORSDOF 6The map FLD file:
# AVS field file
#
# AutoDock Atomic Affinity and Electrostatic Grids
#
# Created by ./autogrid4.
#
#SPACING 0.375
#NELEMENTS 240 240 240
#CENTER 40.649 37.366 48.500
#MACROMOLECULE 1o8a.pdbqt
#GRID_PARAMETER_FILE 1o8a.gpf
#
ndim=3 # number of dimensions in the field
dim1=241 # number of x-elements
dim2=241 # number of y-elements
dim3=241 # number of z-elements
nspace=3 # number of physical coordinates per point
veclen=15 # number of affinity values at each point
data=float # data type (byte, integer, float, double)
field=uniform # field type (uniform, rectilinear, irregular)
coord 1 file=1o8a.maps.xyz filetype=ascii offset=0
coord 2 file=1o8a.maps.xyz filetype=ascii offset=2
coord 3 file=1o8a.maps.xyz filetype=ascii offset=4
label=HD-affinity # component label for variable 1
label=C-affinity # component label for variable 2
label=A-affinity # component label for variable 3
label=N-affinity # component label for variable 4
label=NA-affinity # component label for variable 5
label=OA-affinity # component label for variable 6
label=F-affinity # component label for variable 7
label=P-affinity # component label for variable 8
label=SA-affinity # component label for variable 9
label=S-affinity # component label for variable 10
label=Cl-affinity # component label for variable 11
label=Br-affinity # component label for variable 12
label=I-affinity # component label for variable 13
label=Electrostatics # component label for variable 13
label=Desolvation # component label for variable 14
#
# location of affinity grid files and how to read them
#
variable 1 file=1o8a.HD.map filetype=ascii skip=6
variable 2 file=1o8a.C.map filetype=ascii skip=6
variable 3 file=1o8a.A.map filetype=ascii skip=6
variable 4 file=1o8a.N.map filetype=ascii skip=6
variable 5 file=1o8a.NA.map filetype=ascii skip=6
variable 6 file=1o8a.OA.map filetype=ascii skip=6
variable 7 file=1o8a.F.map filetype=ascii skip=6
variable 8 file=1o8a.P.map filetype=ascii skip=6
variable 9 file=1o8a.SA.map filetype=ascii skip=6
variable 10 file=1o8a.S.map filetype=ascii skip=6
variable 11 file=1o8a.Cl.map filetype=ascii skip=6
variable 12 file=1o8a.Br.map filetype=ascii skip=6
variable 13 file=1o8a.I.map filetype=ascii skip=6
variable 14 file=1o8a.e.map filetype=ascii skip=6
variable 15 file=1o8a.d.map filetype=ascii skip=6The GPF file:
npts 240 240 240
gridfld 1o8a.maps.fld
spacing 0.375
receptor_types A C HD N OA SA
ligand_types HD C A N NA OA F P SA S Cl Br I
receptor 1o8a.pdbqt
gridcenter 40.649 37.366 48.500
smooth 0.5
map 1o8a.HD.map
map 1o8a.C.map
map 1o8a.A.map
map 1o8a.N.map
map 1o8a.NA.map
map 1o8a.OA.map
map 1o8a.F.map
map 1o8a.P.map
map 1o8a.SA.map
map 1o8a.S.map
map 1o8a.Cl.map
map 1o8a.Br.map
map 1o8a.I.map
elecmap 1o8a.e.map
dsolvmap 1o8a.d.map
dielectric -0.1465I didn't use a DPF file. The hardware that I'm using is NVIDIA A40. Thank you!
Yuwei-Pan
commented
2 months ago @Yuwei-Pan Which version of AD-GPU are you using and what GPU are you running on?
I'm using autodock_gpu_128wi and I'm running on NVIDIA A40.
rwxayheee
commented
2 months ago Hi @Yuwei-Pan Could you post the version, kernel and device information (usually printed at the beginning of the output)? The dev @atillack might be able to provide better advice
npts 240 240 240
This is a really large box and can encompass the entire protein. Have you tried reducing the size of the box (maybe to 40, 40, 40) and see if that works?
rwxayheee
commented
2 months ago Hey @Yuwei-Pan
I was able to reproduce this and I think the reason is the ordering of atoms in the ligand PDBQT file, as @diogomart commented in #224. It worked just fine in the 240x240x240 box with this ligand PDBQT file
REMARK 6 active torsions:
REMARK status: ('A' for Active; 'I' for Inactive)
REMARK 1 A between atoms: CA_3 and C_14
REMARK 2 A between atoms: C_4 and S_20
REMARK 3 A between atoms: C_5 and O_16
REMARK 4 A between atoms: C_6 and O_17
REMARK 5 A between atoms: C_7 and C_8
REMARK 6 A between atoms: C_14 and O_18
ROOT
ATOM 1 N UNL 1 9.744 4.280 6.192 0.00 0.00 -0.235 NA
ATOM 2 CA UNL 1 9.395 3.224 6.919 0.00 0.00 0.150 A
ATOM 3 C UNL 1 10.266 2.510 7.756 0.00 0.00 0.073 A
ATOM 4 C UNL 1 11.600 2.927 7.779 0.00 0.00 0.125 A
ATOM 5 C UNL 1 11.995 4.026 7.001 0.00 0.00 0.132 A
ATOM 6 C UNL 1 11.026 4.686 6.230 0.00 0.00 0.125 A
ENDROOT
BRANCH 6 7
ATOM 7 C UNL 1 11.370 5.825 5.378 0.00 0.00 0.127 A
ATOM 8 N UNL 1 10.407 6.399 4.526 0.00 0.00 -0.222 NA
ATOM 9 C UNL 1 11.027 7.346 3.891 0.00 0.00 0.159 A
ATOM 10 O UNL 1 12.329 7.458 4.240 0.00 0.00 -0.289 OA
ATOM 11 C UNL 1 10.500 8.266 2.857 0.00 0.00 0.080 C
ATOM 12 C UNL 1 12.537 6.484 5.191 0.00 0.00 0.145 A
ENDBRANCH 6 7
BRANCH 5 13
ATOM 13 O UNL 1 13.268 4.468 6.969 0.00 0.00 -0.356 OA
ATOM 14 H UNL 1 13.836 3.910 7.238 0.00 0.00 0.218 HD
ENDBRANCH 5 13
BRANCH 2 15
ATOM 15 C UNL 1 7.939 2.838 6.769 0.00 0.00 0.197 C
ATOM 16 OXT UNL 1 7.102 3.184 7.583 0.00 0.00 -0.645 OA
BRANCH 15 17
ATOM 17 O UNL 1 7.705 2.162 5.679 0.00 0.00 -0.772 OA
ATOM 18 H UNL 1 6.845 2.035 5.590 0.00 0.00 0.167 HD
ENDBRANCH 15 17
ENDBRANCH 2 15
BRANCH 4 19
ATOM 19 O UNL 1 12.592 2.263 8.443 0.00 0.00 -0.326 OA
ATOM 20 C UNL 1 12.679 2.468 9.833 0.00 0.00 0.181 C
ENDBRANCH 4 19
BRANCH 3 21
ATOM 21 S UNL 1 9.699 1.088 8.651 0.00 0.00 -0.109 SA
ATOM 22 C UNL 1 8.858 1.887 10.053 0.00 0.00 0.074 C
ENDBRANCH 3 21
TORSDOF 6A quick way to remake ligand PDBQT is to run prepare_ligand on your original PDBQT
./prepare_ligand -l original_ligand.pdbqt -o ordered.pdbqt
atillack
commented
2 months ago Great, thank you for the following up!
Yuwei-Pan
commented
2 months ago Hi @rwxayheee
I tried your suggestion, and it worked well. Thank you very much!
Hello,
I am trying to run a docking of a receptor whose structure was obtained from protein data bank. I deleted all the water and heteroatoms and followed the receptor processing tutorial in AutoDock-Vina. However, I keep getting the following error even when I tried multiple ways of preparing the grid map files.
Running Job #1 Using heuristics: (capped) number of evaluations set to 244898 Local-search chosen method is: ADADELTA (ad)
Rest of Setup time 0.264910s
Executing docking runs, stopping automatically after either reaching 0.15 kcal/mol standard deviation of the best molecules of the last 4 * 5 generations, 42000 generations, or 244898 evaluations:
Generations | Evaluations | Threshold | Average energy of best 10% | Samples | Best Inter + Intra ------------+--------------+------------------+------------------------------+---------+------------------- 0 | 150 | -1.51 kcal/mol | -1.99 +/- 0.33 kcal/mol | 8 | -2.82 kcal/mol autodock_gpu_128wi_a40: ./cuda/kernel_ad.cu:404: void gpu_gradient_minAD(uint32_t, uint32_t, float, float): Assertion `0' failed.
I tried running the docking with the examples provided, and they were fine. I wonder what I'm doing wrong. Thank you!