# PDB file /tmp/499999853.tmp contains no residues

**URL:** <https://ask.bioexcel.eu/t/pdb-file-tmp-499999853-tmp-contains-no-residues/1689>\
**Category:** HADDOCK\
**Created:** [September 26, 2019, 9:24am UTC](https://ask.bioexcel.eu/t/pdb-file-tmp-499999853-tmp-contains-no-residues/1689 "2019-09-26T09:24:56Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![Ayesha\_Fatima](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/ayesha_fatima/32/191_2.png) [@Ayesha\_Fatima](https://ask.bioexcel.eu/u/Ayesha_Fatima)\
**Post date:** [September 26, 2019, 9:24am UTC](https://ask.bioexcel.eu/t/pdb-file-tmp-499999853-tmp-contains-no-residues/1689/1 "2019-09-26T09:24:56Z")

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Good morning. would you kindly let me know what error is this  
thank you

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**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [September 26, 2019, 9:46am UTC](https://ask.bioexcel.eu/t/pdb-file-tmp-499999853-tmp-contains-no-residues/1689/2 "2019-09-26T09:46:17Z")

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No residues found in your PDB, probably a problem with your input PDB…  
But without more info about what you are docking we can’t help you more.

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<div class="post-metadata">

**Author:** ![Ayesha\_Fatima](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/ayesha_fatima/32/191_2.png) [@Ayesha\_Fatima](https://ask.bioexcel.eu/u/Ayesha_Fatima)\
**Post date:** [September 26, 2019, 10:38am UTC](https://ask.bioexcel.eu/t/pdb-file-tmp-499999853-tmp-contains-no-residues/1689/3 "2019-09-26T10:38:40Z")

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I got this detail  
There was an unknown problem in the processing of your data.  
This is either a server error, or some inconsistency in your input has been detected that was not properly reported.  
If the error message seems meaningless, forward this email to [haddocking@gmail.com](mailto:haddocking@gmail.com)  
Importantly, do provide the following information:

- Which interface are you accessing?
- What is your access level to the HADDOCK server?
- What kind of molecules are you docking?  
The HADDOCK server is in constant development, thank you for your patience.

Error message\>

("\<type ‘exceptions.Exception’\>:", Exception(‘ERROR: PDB file /tmp/499999853.tmp contains no residues\n’,))

Full error information:

Traceback (most recent call last):  
File “/home/enmr/services-enmr/HADDOCK2.2/py/prepare\_haddock.py”, line 105, in   
s = s.convert(HaddockRunData)  
File “haddock::HaddockRunParameters.spy”, line 3576, in convert  
c = spyder.core.convert(HaddockRunParameters, target, self, deepcopy)  
File “spyder.modules.core::pathing.py”, line 267, in convert  
ret = do\_convert(i,o,arg)  
File “spyder.modules.core::pathing.py”, line 254, in do\_convert  
conv = execute\_path(i,arg,path,failed,visited,None,0,None)  
File “spyder.modules.core::pathing.py”, line 174, in execute\_path  
result = execute\_path(c.outtype, arg, pathtail, failed, visited, method,splitcounter,methodindex)  
File “spyder.modules.core::pathing.py”, line 159, in execute\_path  
result = f(arg)  
File “haddock::haddockserver.py”, line 172, in parameters\_to\_rundata  
r2.passivereslist = spyder.atom.determine\_passive\_residues(r2.activereslist, surfacelist, pdb, i.auto\_passive\_radius)  
File “spyder.modules.atom::determine\_passive\_residues.py”, line 3, in determine\_passive\_residues  
distances = pdb.convert(InterResidueDistanceArray)  
File “spyder.modules.builtin::Data.py”, line 61, in convert  
else: return spyder.core.convert(type(self),target, self, globals())  
File “spyder.modules.core::pathing.py”, line 267, in convert  
ret = do\_convert(i,o,arg)  
File “spyder.modules.core::pathing.py”, line 254, in do\_convert  
conv = execute\_path(i,arg,path,failed,visited,None,0,None)  
File “spyder.modules.core::pathing.py”, line 159, in execute\_path  
result = f(arg)  
File “spyder.modules.atom::atom.spy”, line 8830, in spyderconverterfunction\_4  
if s.err is not None: raise Exception(s.err)  
Exception: ERROR: PDB file /tmp/499999853.tmp contains no residues

I would appreciate the help

Thank you

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<div class="post-metadata">

**Author:** ![amjjbonvin](https://dub1.discourse-cdn.com/flex013/user_avatar/ask.bioexcel.eu/amjjbonvin/32/23_2.png) [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)\
**Post date:** [September 26, 2019, 10:59am UTC](https://ask.bioexcel.eu/t/pdb-file-tmp-499999853-tmp-contains-no-residues/1689/4 "2019-09-26T10:59:17Z")

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Read the error message… and do provide the requested information…