Hi Nawel, This typically means that there is some kind of connectivity problem in one of the structures. If you sent me the two structures (Representative_confo_site_active_minimum_distance_state001.pdb and DB08734_1|LigPrep_output_named|sdf|8330|dock5) I might be able to provide a more precise diagnosis of the problem. —Eric Eric Pettersen UCSF Computer Graphics Lab

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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