On Aug 7, 2018, at 2:16 AM, Nawel Mele <nawel.mele@gmail.com> wrote:

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.

Nawel

Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
    #0 Representative_confo_site_active_minimum_distance_state001.pdb
    #1 DB08734_1|LigPrep_output_named|sdf|8330|dock5

H-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/A
2 hydrogen bonds found
DB08734_1|LigPrep_output_named|sdf|8330|dock6 opened
donor: #0 ASN 76.A ND2  acceptor: #1 UNK 1 N4
Traceback (most recent call last):
  File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/chimeraInit.py", line 683, in init
    chimera.openModels.open(a, prefixableType=1)
  File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/chimera/__init__.py", line 1919, in open
    models = func(filename, *args, **kw)
  File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/ChimeraExtension.py", line 35, in func
    processCommandFile(cmdFile)
  File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 108, in processCommandFile
    _processFile(f, emulateRead, filename)
  File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 143, in _processFile
    if makeCommand(line):
  File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 69, in makeCommand
    f(c, args)
  File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/ChimeraExtension.py", line 33, in cmdHBonds
    specInfo=[("spec", "models", "molecules")])
  File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 451, in doExtensionFunc
    extFunc(*tuple(processedArgs), **kw)
  File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 940, in createHBonds
    interSubmodel=interSubmodel, cacheDA=cacheDA)
  File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", 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 "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", 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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