<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Nawel,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>This <i class="">typically</i> 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.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space: pre;"> </span>UCSF Computer Graphics Lab</div></div><br class="Apple-interchange-newline">
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<div><br class=""><blockquote type="cite" class=""><div class="">On Aug 7, 2018, at 2:16 AM, Nawel Mele <<a href="mailto:nawel.mele@gmail.com" class="">nawel.mele@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class="">Dear Chimera Users<br class=""><br class=""></div>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.<br class=""><br class=""></div>Many thanks for your help.<br class=""><br class=""></div>Nawel<br class=""><div class=""><div class=""><br class=""><span style="color:rgb(0,0,255)" class=""><i class="">Finding intermodel H-bonds<br class="">Finding intramodel H-bonds<br class="">Constraints relaxed by 0.4 angstroms and 20 degrees<br class="">Models used:<br class=""> #0 Representative_confo_site_active_minimum_distance_state001.pdb<br class=""> #1 DB08734_1|LigPrep_output_named|sdf|8330|dock5<br class=""><br class="">H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):<br class="">#0 LYS 73.A NZ #1 UNK 1 O1 no hydrogen 2.924 N/A<br class="">#0 ASN 76.A ND2 #1 UNK 1 N4 no hydrogen 2.398 N/A<br class="">2 hydrogen bonds found<br class="">DB08734_1|LigPrep_output_named|sdf|8330|dock6 opened<br class="">donor: #0 ASN 76.A ND2 acceptor: #1 UNK 1 N4<br class="">Traceback (most recent call last):<br class=""> File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/chimeraInit.py", line 683, in init<br class=""> chimera.openModels.open(a, prefixableType=1)<br class=""> File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/chimera/__init__.py", line 1919, in open<br class=""> models = func(filename, *args, **kw)<br class=""> File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/ChimeraExtension.py", line 35, in func<br class=""> processCommandFile(cmdFile)<br class=""> File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 108, in processCommandFile<br class=""> _processFile(f, emulateRead, filename)<br class=""> File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 143, in _processFile<br class=""> if makeCommand(line):<br class=""> File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 69, in makeCommand<br class=""> f(c, args)<br class=""> File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/ChimeraExtension.py", line 33, in cmdHBonds<br class=""> specInfo=[("spec", "models", "molecules")])<br class=""> File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/Midas/midas_text.py", line 451, in doExtensionFunc<br class=""> extFunc(*tuple(processedArgs), **kw)<br class=""> File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 940, in createHBonds<br class=""> interSubmodel=interSubmodel, cacheDA=cacheDA)<br class=""> File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 574, in findHBonds<br class=""> (donorAtom, donorHyds) + args):<br class="">TypeError: accPhiPsi() takes exactly 8 arguments (9 given)<br class="">Error while processing chimera_input_step2_bug.cmd:<br class="">TypeError: accPhiPsi() takes exactly 8 arguments (9 given)<br class=""><br class=""> File "/sge/packs/binaries_centos/chimera-1.11.2-CentOS6/share/FindHBond/base.py", line 574, in findHBonds<br class=""> (donorAtom, donorHyds) + args):<br class=""><br class="">See reply log for Python traceback.<br class=""></i></span><br class=""><br class=""><br clear="all" class=""><div class=""><div class=""><br class="">-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><p style="text-align:left" class=""><font face="times new roman, serif" class="">Dr Nawel Mele, </font></p></div></div></div></div></div><span style="font-family:"times new roman",serif" class="">T: +33 (0) 634443794 (Fr)</span><br class=""><div class=""><div class=""><div class=""><div class=""><div class=""><p style="text-align:left" class=""><span style="font-family:"times new roman",serif" class="">+44 (0) 7704331840 (UK)</span></p></div></div></div></div></div><div class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><div dir="ltr" class=""><p style="text-align:left" class=""><font face="times new roman, serif" class=""><br class=""></font></p></div></div></div></div></div></div></div>
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