AutoDockTools (ADT) Problems

[Sarangian Ravichandran <ravichsa |-at-| UMDNJ.EDU>]

Hi All:
 I have some difficulty in using AutoDockTools, ADT
 developed by Dr. M. Sanner.
 I have installed ADT in SGI(Octane2), and have
 been trying to redo the examples that came with AutoDock
 (3ptb and 1hvr sample systems) using ADT. When I
 read the receptor using the module AutoGpf of ADT, I am
 getting error messages (see below) for both 3ptb and
 1hvr. I have attached only the error message for 1hvr
 and I get similar messages for 3ptb system.
 I would like to know any ADT user have experienced
 similar problems. Any help is greatly appreciated.
 regards,
 Ravi
 Email: ravichsa |-at-| umdnj.edu
 ------------------------------
 1hvr.pdbqs:
 ----------
 I used AutoGpf to read the 1hvr.pdbqs file
 and the options I choose were to automatically
 merge non-polar Hs, to automatically merge lone-pairs
 , and save save the result as 1hvr.pdbqs
 non-integeral charge on 1hvr is 3.992, I hit ok and
 I get the following message in the python shell
 ---------------------------------
 >>>
 Warning: interruption in backbone between 1hvr:
 :PHE99:N and 1hvr: :HYD100:H of 380 Angstrom
 Warning: interruption in backbone between 1hvr:
 :HYD100:H and 1hvr: :PRO101:O of 423 Angstrom
 Warning: interruption in backbone between 1hvr:
 :PHE199:N and 1hvr: :HYD200:O of 380 Angstrom
 Exception in Tkinter callback
 Traceback (innermost last):
 File
 "/usr/people/ravi/FINALADT/share/lib/python1.5/lib-tk/Tkinter.py",
 line 764, in __call__
  return apply(self.func, args)
  File
 "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/
 AutoDockTools/autogpfCommands.py",
 line 761, in guiCallback
 mergeLPS=mergeLPS, newfilename=newfilename, checkMTypes=1, log=1,
 redraw=1)
 File
 "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/
 ViewerFramework/VFCommand.py",
 line 582, in doitWrapper
 result = apply( self.vf.tryto, (self.func,)+args, kw )
  File
 "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/
 ViewerFramework/VF.py",
 line 553, in tryto result = apply( command, args, kw )
 File
 "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/
 AutoDockTools/autogpfCommands.py",
 line 798, in doit apply(self.vf.ADgpf_initMacro, (mol,), kw)
   File
 "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/
 AutoDockTools/autogpfCommands.py",
 line 314, in __call__apply(self.doitWrapper,(mol,), kw)
   File
 "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/
 ViewerFramework/VFCommand.py",
 line 582, in doitWrapper
 result = apply( self.vf.tryto, (self.func,)+args, kw )File
 "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/
 ViewerFramework/VF.py",
 line 553, in tryto result = apply( command, args, kw )
 File
 "/usr/people/ravi/FINALADT/share/lib/python1.5/site-packages/
 AutoDockTools/autogpfCommands.py",
 line 350, in doit
 if hasLPS and not mergeNPHS and not addSolPar:NameError: hasLPS
 ------------------------------