Unknow errors when ADCP run in shell

[mengskl]

I performed ADCP in shell script which aim to do some high throughput virtual screening. But i found that ADCP did not work in script.

here is my input in command line:

adcp -t protein.trg -s GGGGGGGG -N 100 -n 2500000 -o output.pdb

The output results can be obtained under the above command.

But ADCP did not work when the same command was written into script:

!/bin/bash

adcp -t protein.trg -s GGGGGGGG -N 100 -n 2500000 -o output.pdb run the script by> bash script.sh

The output were show as follow: Detected 112 cores, request 112 cores, using 112 cores copying the ramaprob.data file from /software/autodock/crankpep/ADFRsuite_x86_64Linux_1.0/CCSBpckgs/ADCP/ramaprob.data to /test/adcp Performing search (100 ADCP runs with 2500000 steps each) ... 0% 10 20 30 40 50 60 70 80 90 100% |----|----|----|----|----|----|----|----|----|----| 10 ENDED WITH ERROR 10 err 11 ENDED WITH ERROR 11 err 75 ENDED WITH ERROR 75 err 13 ENDED WITH ERROR 13 err 14 ENDED WITH ERROR 14 err 78 ENDED WITH ERROR 78 err 79 ENDED WITH ERROR 79 err 80 ENDED WITH ERROR 80 err 81 ENDED WITH ERROR 81 err 19 ENDED WITH ERROR 19 err 83 ENDED WITH ERROR 83 err 31 ENDED WITH ERROR 31 err 32 ENDED WITH ERROR 32 err 33 ENDED WITH ERROR 33 err 34 ENDED WITH ERROR 34 err 35 ENDED WITH ERROR 35 err 21 ENDED WITH ERROR 21 err 36 ENDED WITH ERROR 36 err 37 ENDED WITH ERROR 37 err 38 ENDED WITH ERROR 38 err 39 ENDED WITH ERROR 39 err 40 ENDED WITH ERROR 40 err 41 ENDED WITH ERROR 41 err 22 ENDED WITH ERROR 22 err 42 ENDED WITH ERROR 42 err 43 ENDED WITH ERROR 43 err 64 ENDED WITH ERROR 64 err 44 ENDED WITH ERROR 44 err 45 ENDED WITH ERROR 45 err 46 ENDED WITH ERROR 46 err 47 ENDED WITH ERROR 47 err 86 ENDED WITH ERROR 86 err 0 ENDED WITH ERROR 0 err 49 ENDED WITH ERROR 49 err 65 ENDED WITH ERROR 65 err 50 ENDED WITH ERROR 50 err 51 ENDED WITH ERROR 51 err 52 ENDED WITH ERROR 52 err 53 ENDED WITH ERROR 53 err 87 ENDED WITH ERROR 87 err 54 ENDED WITH ERROR 54 err 55 ENDED WITH ERROR 55 err 66 ENDED WITH ERROR 66 err 56 ENDED WITH ERROR 56 err 57 ENDED WITH ERROR 57 err 58 ENDED WITH ERROR 58 err 59 ENDED WITH ERROR 59 err 88 ENDED WITH ERROR 88 err 60 ENDED WITH ERROR 60 err 61 ENDED WITH ERROR 61 err 67 ENDED WITH ERROR** 67 err 62 ENDED WITH ERROR** 62 err 63 ENDED WITH ERROR* 63 err 1 ENDED WITH ERROR**** 1 err 2 ENDED WITH ERROR*** 2 err 89 ENDED WITH ERROR**** 89 err 3 ENDED WITH ERROR** 3 err 4 ENDED WITH ERROR** 4 err 68 ENDED WITH ERROR* 68 err 5 ENDED WITH ERROR*** 5 err 6 ENDED WITH ERROR**** 6 err 7 ENDED WITH ERROR**** 7 err 8 ENDED WITH ERROR 8 err 9 ENDED WITH ERROR 9 err 73 ENDED WITH ERROR 73 err 69 ENDED WITH ERROR 69 err 74 ENDED WITH ERROR** 74 err 12 ENDED WITH ERROR** 12 err 48 ENDED WITH ERROR 48 err 76 ENDED WITH ERROR 76 err 77 ENDED WITH ERROR**** 77 err 15 ENDED WITH ERROR**** 15 err 16 ENDED WITH ERROR 16 err 70 ENDED WITH ERROR 70 err 17 ENDED WITH ERROR** 17 err 18 ENDED WITH ERROR** 18 err 82 ENDED WITH ERROR 82 err 20 ENDED WITH ERROR 20 err 84 ENDED WITH ERROR**** 84 err 85 ENDED WITH ERROR**** 85 err 71 ENDED WITH ERROR 71 err 23 ENDED WITH ERROR 23 err 24 ENDED WITH ERROR** 24 err 25 ENDED WITH ERROR** 25 err 26 ENDED WITH ERROR 26 err 27 ENDED WITH ERROR 27 err 28 ENDED WITH ERROR**** 28 err 72 ENDED WITH ERROR**** 72 err 29 ENDED WITH ERROR 29 err 30 ENDED WITH ERROR 30 err 94 ENDED WITH ERROR** 94 err 95 ENDED WITH ERROR** 95 err 96 ENDED WITH ERROR 96 err 97 ENDED WITH ERROR 97 err 98 ENDED WITH ERROR**** 98 err 99 ENDED WITH ERROR**** 99 err 90 ENDED WITH ERROR 90 err 91 ENDED WITH ERROR 91 err 92 ENDED WITH ERROR** 92 err 93 ENDED WITH ERROR** 93 err Docking performed in 2.50 seconds, i.e. 0 hours 00 minutes 02.496685 seconds Traceback (most recent call last): File "/software/autodock/crankpep/ADFRsuite_x86_64Linux_1.0/CCSBpckgs/ADCP/runADCP.py", line 464, in runner(kw) File "/software/autodock/crankpep/ADFRsuite_x86_64Linux_1.0/CCSBpckgs/ADCP/runADCP.py", line 406, in call runner(kw) File "/software/autodock/crankpep/ADFRsuite_x86_64Linux_1.0/CCSBpckgs/ADCP/clusterADCP.py", line 164, in call models = Read(syst) File "/software/autodock/crankpep/ADFRsuite_x86_64Linux_1.0/CCSBpckgs/MolKit2/init.py", line 63, in Read mol = readWithPrody(filename, header=header, model=model) File "/software/autodock/crankpep/ADFRsuite_x86_64Linux_1.0/CCSBpckgs/MolKit2/init.py", line 98, in readWithPrody mol.buildBondsByDistance() File "/software/autodock/crankpep/ADFRsuite_x86_64Linux_1.0/CCSBpckgs/MolKit2/molecule.py", line 913, in buildBondsByDistance bo = self.getBondOrdRadius() File "/software/autodock/crankpep/ADFRsuite_x86_64Linux_1.0/CCSBpckgs/MolKit2/molecule.py", line 1286, in getBondOrdRadius return self.bo_rad[self._ag.getData('atomicNumber')] AttributeError: Molecule instance has no attribute '_ag'

========================================================= All the output file have the same context: found external potential parameters 1 found external potential parameters 4 setting constrained list file constrains Building protein from sequence: ABCDEFGHIGKLMNGPQRSTGVWGYZ. Building protein from sequence: ABCDEFGHIGKLMNGPQRSTGVWGYZ (26 amino acids, 1 chains). ABCDEFGHIGKLMNGPQRSTGVWGYZ 26 INFO: Attempting a serial MC simulation. eof return ERROR! ERROR! EOF while reading in from input PDB file. ramaprob initialise success

=========================================================

How can i solve this issues?

[sachinpujeri]

Even I have the same error Can u help whoever has resolved this issue

[Type59pro]

run ${ADCP_PATH}/bin/python -c "import sys;print(sys.maxunicode)"

if the output is 1114111, it means you python is using UCS4. you need recomplie numpy from source.

run:

remove numpy

${ADCP_PATH}/bin/python -m pip uninstall numpy

download numpy source code

wget https://github.com/numpy/numpy/archive/v1.16.6.tar.gz

extract source code

tar -xvzf v1.16.6.tar.gz

enter extracted directory

cd numpy-1.16.6

install the build numpy

${ADCP_PATH}/bin/python -m pip install cython ${ADCP_PATH}/bin/python setup.py build

after completing these steps, run adcp to see if the error has been resolved