[Chimera-users] Problem with FIndHBonds

Nawel Mele nawel.mele at gmail.com
Tue Aug 7 02:16:18 PDT 2018

Dear Chimera Users

I am using hbond command to determine hydrogen bonds between a receptor and
multiple  compounds with different conformations from a docking simulation.
I used a cmd script to automatise the process however I am facing and error
that I am not sure to understand. I just pasted follow the part of the
reply log where the problem appeared. The problem here is that when I load
the compound with the different docked conformations separatly it is not
always the same conformation taht has this error so I don't know what is
the real problem.

Many thanks for your help.


*Finding intermodel H-bondsFinding intramodel H-bondsConstraints relaxed by
0.4 angstroms and 20 degreesModels used:    #0
Representative_confo_site_active_minimum_distance_state001.pdb    #1
DB08734_1|LigPrep_output_named|sdf|8330|dock5H-bonds (donor, acceptor,
hydrogen, D..A dist, D-H..A dist):#0 LYS 73.A NZ   #1 UNK 1 O1  no
hydrogen  2.924  N/A#0 ASN 76.A ND2  #1 UNK 1 N4  no hydrogen  2.398  N/A2
hydrogen bonds foundDB08734_1|LigPrep_output_named|sdf|8330|dock6
openeddonor: #0 ASN 76.A ND2  acceptor: #1 UNK 1 N4Traceback (most recent
call last):  File
line 683, in init    chimera.openModels.open(a, prefixableType=1)  File
line 1919, in open    models = func(filename, *args, **kw)  File
line 35, in func    processCommandFile(cmdFile)  File
line 108, in processCommandFile    _processFile(f, emulateRead, filename)
line 143, in _processFile    if makeCommand(line):  File
line 69, in makeCommand    f(c, args)  File
line 33, in cmdHBonds    specInfo=[("spec", "models", "molecules")])  File
line 451, in doExtensionFunc    extFunc(*tuple(processedArgs), **kw)  File
line 940, in createHBonds    interSubmodel=interSubmodel, cacheDA=cacheDA)
line 574, in findHBonds    (donorAtom, donorHyds) + args):TypeError:
accPhiPsi() takes exactly 8 arguments (9 given)Error while processing
chimera_input_step2_bug.cmd:TypeError: accPhiPsi() takes exactly 8
arguments (9 given)  File
line 574, in findHBonds    (donorAtom, donorHyds) + args):See reply log for
Python traceback.*


Dr Nawel Mele,
T: +33 (0) 634443794 (Fr)

+44 (0) 7704331840 (UK)
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