ADL: ADT question --> merge non-polar hydrogens

Jade Hatley Jade.M.Hatley at
Mon Mar 24 13:03:44 PDT 2008

I am trying to load a apoprotein .pdb into ADT in order to merge non-polar
hydrogens, add charges, and save as .pdbqs.  The .pdb files were created by
NAMD (I changed the appropriate amino acid aliases).  The protein is a P450
and the I split them into an apoprotein.pdb file and a heme.pdb file.  It is
the apo protein file that gives this error.  I've tried to search the
tutorial and FAQs but cannot find anything specific.

If anyone has any ideas or can point me to the section in a manual, I would
really appreciate it.


> Python 2.3.2 (#6, Dec 11 2003, 15:11:30)
> [GCC 2.95.3 20010315 (SuSE)] on linux2
> Type "copyright", "credits" or "license()" for more information.
>     ****************************************************************
>     Personal firewall software may warn about the connection IDLE
>     makes to its subprocess using this computer's internal loopback
>     interface.  This connection is not visible on any external
>     interface and no data is sent to or received from the Internet.
>     ****************************************************************
> IDLE 1.0      ==== No Subprocess ====
>>>> ERROR ************************************************
> Traceback (most recent call last):
>   File 
y", line 582, in tryto
>     result = apply( command, args, kw )
>   File 
, line 1975, in doit
>     npHs = ats.get(lambda x: x.element=='H' and
>   File 
line 157, in get
>     return self.ReturnType(filter(who,
>   File 
, line 1975, in <lambda>
>     npHs = ats.get(lambda x: x.element=='H' and
>   File "/home/cheri/PROGRAMS/ADT/share/lib/python2.3/", line 28, in
>     def __getitem__(self, i): return[i]
> IndexError: list index out of range

Jade M. Hatley
Graduate Student, PhD Candidate
Biochemistry and Molecular Biology
University of Texas - Houston Medical School
MSB 3.316

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