Segmentation Fault (Core Dumped)

[stepha86]

Describe the bug

Some of my ligands.sdf files meet this problem and end up producing empty docking_scores.txt files. May I know how to solve this? The path to my ligands.sdf is stated and in the current working directory.

Thanks.

Expected behavior

Unidock should output the results as docking_scores.txt files and a subdirectory of the processed ligand.sdf

To Reproduce

Sample of my ligands.sdf file
$$$$
CHEMBL492097_sanitized
RDKit 3D

32 34 0 0 1 0 0 0 0 0999 V2000
-2.7806 -0.3008 5.2027 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.7118 -1.0967 5.8028 B 0 0 0 0 0 0 0 0 0 0 0 0
-1.6645 -1.2755 7.2526 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6013 -1.7706 4.8768 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7924 -1.2129 5.1911 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9093 -1.9292 4.4127 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8667 -1.6725 2.8905 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2979 -2.8761 2.1160 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0937 -2.6310 0.6010 C 0 0 2 0 0 0 0 0 0 0 0 0
2.3684 -2.3289 -0.0702 N 0 0 0 0 0 0 0 0 0 0 0 0
2.9805 -1.0249 -0.1403 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3806 -0.0167 0.3211 O 0 0 0 0 0 0 0 0 0 0 0 0
4.3098 -0.8341 -0.7521 C 0 0 0 0 0 0 0 0 0 0 0 0
5.1568 -1.8123 -1.2720 C 0 0 0 0 0 0 0 0 0 0 0 0
6.3335 -1.3434 -1.7685 N 0 0 0 0 0 0 0 0 0 0 0 0
6.4436 -0.0021 -1.6535 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0782 0.6537 -0.9267 S 0 0 0 0 0 0 0 0 0 0 0 0
0.0177 -1.6197 0.2696 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8272 -1.2839 1.1445 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.1173 -1.1408 -1.0780 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.9014 0.0064 -1.4468 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.0439 1.1048 -0.5817 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8018 2.2116 -0.9687 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.4149 2.2408 -2.2228 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2638 1.1636 -3.1131 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4957 0.0532 -2.7169 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9097 1.1944 -4.4494 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.2259 1.6716 -4.5960 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.8349 1.6933 -5.8548 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.1375 1.2447 -6.9789 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.8301 0.7714 -6.8464 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2175 0.7439 -5.5892 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
2 4 1 0
4 5 1 0
5 6 1 0
6 7 1 0
7 8 1 0
9 8 1 1
9 10 1 0
10 11 1 0
11 12 2 0
11 13 1 0
13 14 2 0
14 15 1 0
15 16 2 0
16 17 1 0
13 17 1 0
9 18 1 0
18 19 2 0
18 20 1 0
20 21 1 0
21 22 2 0
22 23 1 0
23 24 2 0
24 25 1 0
25 26 2 0
21 26 1 0
25 27 1 0
27 28 2 0
28 29 1 0
29 30 2 0
30 31 1 0
31 32 2 0
27 32 1 0
M END

(59)
CHEMBL492097

(59)
3.998

<Molecular_Weight> (59)
451.34624

<Num_H_Acceptors> (59)
5

<Num_H_Donors> (59)
4

<Num_RotatableBonds> (59)
11

(59)
0

$$$$
CHEMBL2047619_sanitized
RDKit 3D

32 35 0 0 0 0 0 0 0 0999 V2000
-1.7876 1.6608 4.8846 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.1970 0.4790 4.4996 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.1556 -0.4660 5.3147 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6547 0.3301 3.1748 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7047 1.3971 2.2615 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1926 1.2507 0.9691 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3689 0.0305 0.5618 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4407 -1.0288 1.4782 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0734 -0.8846 2.7696 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8908 -0.1523 -0.8092 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0237 -0.8325 -1.0736 N 0 0 0 0 0 0 0 0 0 0 0 0
2.2520 -0.7669 -2.3776 N 0 0 0 0 0 0 0 0 0 0 0 0
1.2754 -0.0442 -2.9682 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3721 0.3446 -2.0027 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8497 1.1356 -2.2563 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0586 0.8810 -1.7331 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3943 -0.3035 -0.9197 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8004 -1.3971 -1.1213 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.3928 -0.1898 0.1068 N 0 0 0 0 0 0 0 0 0 0 0 0
-3.5841 -1.1658 1.1449 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8048 -0.7316 2.4613 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.9708 -1.6578 3.4947 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.9388 -3.0276 3.2191 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.1596 -4.2921 4.6328 Br 0 0 0 0 0 0 0 0 0 0 0 0
-3.7547 -3.4701 1.9057 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5856 -2.5455 0.8702 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3934 -1.3776 -3.0155 C 0 0 0 0 0 0 0 0 0 0 0 0
3.4700 -1.5051 -4.4176 C 0 0 0 0 0 0 0 0 0 0 0 0
4.5840 -2.1030 -5.0152 C 0 0 0 0 0 0 0 0 0 0 0 0
5.6312 -2.5825 -4.2263 C 0 0 0 0 0 0 0 0 0 0 0 0
5.5660 -2.4681 -2.8366 C 0 0 0 0 0 0 0 0 0 0 0 0
4.4548 -1.8719 -2.2331 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
2 4 1 0
4 5 2 0
5 6 1 0
6 7 2 0
7 8 1 0
8 9 2 0
4 9 1 0
7 10 1 0
10 11 2 0
11 12 1 0
12 13 1 0
13 14 2 0
10 14 1 0
14 15 1 0
15 16 2 0
16 17 1 0
17 18 2 0
17 19 1 0
19 20 1 0
20 21 2 0
21 22 1 0
22 23 2 0
23 24 1 0
23 25 1 0
25 26 2 0
20 26 1 0
12 27 1 0
27 28 2 0
28 29 1 0
29 30 2 0
30 31 1 0
31 32 2 0
27 32 1 0
M CHG 2 1 -1 2 1
M END

(60)
CHEMBL2047619

(60)
5.898

<Molecular_Weight> (60)
489.32078

<Num_H_Acceptors> (60)
4

<Num_H_Donors> (60)
1

<Num_RotatableBonds> (60)
6

(60)
0

$$$$

Environment

Cuda Version
{
"cuda" : {
"name" : "CUDA SDK",
"version" : "12.4.20240228"
},
"cuda_cccl" : {
"name" : "CUDA C++ Core Compute Libraries",
"version" : "12.4.99"
},
"cuda_cudart" : {
"name" : "CUDA Runtime (cudart)",
"version" : "12.4.99"
},
"cuda_cuobjdump" : {
"name" : "cuobjdump",
"version" : "12.4.99"
},
"cuda_cupti" : {
"name" : "CUPTI",
"version" : "12.4.99"
},
"cuda_cuxxfilt" : {
"name" : "CUDA cu++ filt",
"version" : "12.4.99"
},
"cuda_demo_suite" : {
"name" : "CUDA Demo Suite",
"version" : "12.4.99"
},
"cuda_gdb" : {
"name" : "CUDA GDB",
"version" : "12.4.99"
},
"cuda_nsight" : {
"name" : "Nsight Eclipse Plugins",
"version" : "12.4.99"
},
"cuda_nvcc" : {
"name" : "CUDA NVCC",
"version" : "12.4.99"
},
"cuda_nvdisasm" : {
"name" : "CUDA nvdisasm",
"version" : "12.4.99"
},
"cuda_nvml_dev" : {
"name" : "CUDA NVML Headers",
"version" : "12.4.99"
},
"cuda_nvprof" : {
"name" : "CUDA nvprof",
"version" : "12.4.99"
},
"cuda_nvprune" : {
"name" : "CUDA nvprune",
"version" : "12.4.99"
},
"cuda_nvrtc" : {
"name" : "CUDA NVRTC",
"version" : "12.4.99"
},
"cuda_nvtx" : {
"name" : "CUDA NVTX",
"version" : "12.4.99"
},
"cuda_nvvp" : {
"name" : "CUDA NVVP",
"version" : "12.4.99"
},
"cuda_opencl" : {
"name" : "CUDA OpenCL",
"version" : "12.4.99"
},
"cuda_sanitizer_api" : {
"name" : "CUDA Compute Sanitizer API",
"version" : "12.4.99"
},
"libcublas" : {
"name" : "CUDA cuBLAS",
"version" : "12.4.2.65"
},
"libcufft" : {
"name" : "CUDA cuFFT",
"version" : "11.2.0.44"
},
"libcufile" : {
"name" : "GPUDirect Storage (cufile)",
"version" : "1.9.0.20"
},
"libcurand" : {
"name" : "CUDA cuRAND",
"version" : "10.3.5.119"
},
"libcusolver" : {
"name" : "CUDA cuSOLVER",
"version" : "11.6.0.99"
},
"libcusparse" : {
"name" : "CUDA cuSPARSE",
"version" : "12.3.0.142"
},
"libnpp" : {
"name" : "CUDA NPP",
"version" : "12.2.5.2"
},
"libnvfatbin" : {
"name" : "Fatbin interaction library",
"version" : "12.4.99"
},
"libnvjitlink" : {
"name" : "JIT Linker Library",
"version" : "12.4.99"
},
"libnvjpeg" : {
"name" : "CUDA nvJPEG",
"version" : "12.3.1.89"
},
"nsight_compute" : {
"name" : "Nsight Compute",
"version" : "2024.1.0.13"
},
"nsight_systems" : {
"name" : "Nsight Systems",
"version" : "2023.4.4.54"
},
"nvidia_driver" : {
"name" : "NVIDIA Linux Driver",
"version" : "550.54.14"
},
"nvidia_fs" : {
"name" : "NVIDIA file-system",
"version" : "2.19.6"
}
}

Additional Context

No response