[Biopython] Problem with ResidueDepth class

[Carlos Henrique]

Hello everyone,
I have been struggling with the calculation of Residue depth using the
class ResidueDepth as mentioned in [1
<http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ#How_do_I_calculate_residue_depth.3F>
].
I already set everything up and installed the msms from [2
<http://mgltools.scripps.edu/downloads#msms>].
However, I cannot make it run as it should. At first I thought it could be
a problem with my .pdb files, but I tested with 3 different files
downloaded directly from the protein data bank (1YRK, 1B4F, 1U46) and I
keep getting the same error message which is something like this:

A bunch of this:
pdb_to_xyzr: error, file 1YRK.pdb line 1687 residue   37 atom pattern HOH O
was not found in ./atmtypenumbers
pdb_to_xyzr: error, file 1YRK.pdb line 1688 residue   38 atom pattern HOH O
was not found in ./atmtypenumbers
pdb_to_xyzr: error, file 1YRK.pdb line 1689 residue   39 atom pattern HOH O
was not found in ./atmtypenumbers
pdb_to_xyzr: error, file 1YRK.pdb line 1690 residue   40 atom pattern HOH O
was not found in ./atmtypenumbers
pdb_to_xyzr: error, file 1YRK.pdb line 1691 residue   41 atom pattern HOH O
was not found in ./atmtypenumbers
pdb_to_xyzr: error, file 1YRK.pdb line 1692 residue   42 atom pattern HOH O
was not found in ./atmtypenumbers

and the traceback error message right after:
Traceback (most recent call last):
  File "generate_measurements.py", line 82, in <module>
    rd = ResidueDepth(struct[0], '1YRK.pdb')
  File
"/home/carlos/.virtualenvs/pdb/local/lib/python2.7/site-packages/Bio/PDB/ResidueDepth.py",
line 144, in __init__
    surface=get_surface(pdb_file)
  File
"/home/carlos/.virtualenvs/pdb/local/lib/python2.7/site-packages/Bio/PDB/ResidueDepth.py",
line 90, in get_surface
    "Failed to generate surface file using command:\n%s" % make_surface
AssertionError: Failed to generate surface file using command:
msms -probe_radius 1.5 -if /tmp/tmpwodW16 -of /tmp/tmpCbMTwN >
/tmp/tmprkvaQv

I have been trying to solve this since yesterday in vain. Does anyone have
any clue or maybe I can get the residue depth using something else?

Cheers,

[1]
http://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ#How_do_I_calculate_residue_depth.3F
[2] http://mgltools.scripps.edu/downloads#msms

-- 
Carlos Rodrigues
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