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[分子对接] DOCKovalent共价对接时 配体准备时 无法生成

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发表于 Post on 2021-12-6 14:51:05 | 显示全部楼层 Show all |阅读模式 Reading model
使用DOCKovalent共价对接过程中,准备配体时出错

-->$ $DOCKBASE/ligand/generate/build_smiles_ligand.sh lig.smi --covalent
lig
Building xtal-lig​
~/COV/lig_db2/xtal-lig ~/COV/lig_db2


Generating protomers using Marvin (ChemAxon):
INFO:root:Running /yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO -H 7.4 -C false -t dist
DEBUG:sh.command:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">: starting process
DEBUG:sh.command.process:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">.<Process 17949 ['/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc', 'dominanttautomerdistribution', 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO', '-H', '7.4', '-C', 'false', '-t', 'dist']>: started process
DEBUG:sh.command.process.streamwriter:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">.<Process 17949 ['/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc', 'dominanttautomerdistribution', 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO', '-H', '7.4', '-C', 'false', '-t', 'dist']>.stdin: parsed stdin as a None
INFO:sh.command:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist", pid 17949>: process started
DEBUG:sh.command.process:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">.<Process 17949 ['/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc', 'dominanttautomerdistribution', 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO', '-H', '7.4', '-C', 'false', '-t', 'dist']>: <sh.StreamWriter object at 0x2b2418b6e150> ready for more input
DEBUG:sh.command.process:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">.<Process 17949 ['/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc', 'dominanttautomerdistribution', 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO', '-H', '7.4', '-C', 'false', '-t', 'dist']>: acquiring wait lock to wait for completion
DEBUG:sh.command.process.streamwriter:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">.<Process 17949 ['/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc', 'dominanttautomerdistribution', 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO', '-H', '7.4', '-C', 'false', '-t', 'dist']>.stdin: done reading
DEBUG:sh.command.process:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">.<Process 17949 ['/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc', 'dominanttautomerdistribution', 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO', '-H', '7.4', '-C', 'false', '-t', 'dist']>: got wait lock
DEBUG:sh.command.process.streamwriter:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">.<Process 17949 ['/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc', 'dominanttautomerdistribution', 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO', '-H', '7.4', '-C', 'false', '-t', 'dist']>.stdin: closing, but flushing first
DEBUG:sh.command.process:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">.<Process 17949 ['/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc', 'dominanttautomerdistribution', 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO', '-H', '7.4', '-C', 'false', '-t', 'dist']>: exit code not set, waiting on pid
DEBUG:sh.stream_bufferer:acquiring buffering lock for flushing buffer
DEBUG:sh.stream_bufferer:got buffering lock for flushing buffer
DEBUG:sh.stream_bufferer:released buffering lock for flushing buffer
DEBUG:sh.command.process.streamwriter:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">.<Process 17949 ['/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc', 'dominanttautomerdistribution', 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO', '-H', '7.4', '-C', 'false', '-t', 'dist']>.stdin: got chunk size 0 to flush: ''
DEBUG:sh.command.process:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">.<Process 17949 ['/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc', 'dominanttautomerdistribution', 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO', '-H', '7.4', '-C', 'false', '-t', 'dist']>: <sh.StreamReader object at 0x2b2418b6e310> ready to be read from
DEBUG:sh.streamreader:got chunk size 1024: '[#6]-[#8]-[#6](=O)-[#6](C#N)-['
DEBUG:sh.stream_bufferer:acquiring buffering lock to process chunk (buffering: 1)
DEBUG:sh.stream_bufferer:got buffering lock to process chunk (buffering: 1)
DEBUG:sh.stream_bufferer:released buffering lock for processing chunk (buffering: 1)
DEBUG:sh.command.process:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">.<Process 17949 ['/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc', 'dominanttautomerdistribution', 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO', '-H', '7.4', '-C', 'false', '-t', 'dist']>: <sh.StreamReader object at 0x2b2418b6e310> ready to be read from
DEBUG:sh.streamreader:got chunk size 322: 'kUnit.call(CompositeWorkUnit.j'
DEBUG:sh.stream_bufferer:acquiring buffering lock to process chunk (buffering: 1)
DEBUG:sh.stream_bufferer:got buffering lock to process chunk (buffering: 1)
DEBUG:sh.stream_bufferer:released buffering lock for processing chunk (buffering: 1)
DEBUG:sh.command.process:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist">.<Process 17949 ['/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc', 'dominanttautomerdistribution', 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO', '-H', '7.4', '-C', 'false', '-t', 'dist']>: <sh.StreamReader object at 0x2b2418b6e310> ready to be read from
DEBUG:sh.streamreader:got no chunk, done reading
DEBUG:sh.stream_bufferer:acquiring buffering lock for flushing buffer
DEBUG:sh.stream_bufferer:got buffering lock for flushing buffer
DEBUG:sh.stream_bufferer:released buffering lock for flushing buffer
DEBUG:sh.streamreader:got chunk size 0 to flush: ''
DEBUG:sh.command:<Command u"/yp_home/public/soft/multifunction_soft/ChemAxon/JChem/bin/cxcalc dominanttautomerdistribution 'COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO' -H 7.4 -C false -t dist", pid 17949>: process completed
COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO failed to generate tautomer: _cxcalc.dominanttautomerdistribution.bake(smiles, H=pH, C='false', t='dist', _piped=True)
0 xtal-lig-protonated.ism protomers generated


Skipping, No protamers generated
~/COV/lig_db2
Finalizing...
mv: cannot stat `lig-swap.db2': No such file or directory


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