[Chimera-users] Problem with FIndHBonds

[Eric Pettersen]

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 at 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)
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20180807/d34dc48d/attachment.html>