[MMTK] adding pdb file to universe

Ivan Vyalov vyalov at mis.mpg.de
Wed Feb 1 16:02:30 UTC 2012


Dear all,

I'd like to read PDB file with configuration of my system and then to 
treat it by means of MMTK. To achieve this, as far as I understand, one 
should read the PDB file and create MMTK objects which then must be 
passed to universe. However, I have encountered the following problem: 
MMTK does not recognize atom types when I want to create a universe from 
PDB. Another option is that I'm completely missing something. Could 
someone help me with an advice? Here is the code:
|
#!/usr/bin/env python
import pdb,sys,MMTK
from MMTK import *
from MMTK.PDB import PDBConfiguration
from MMTK.ForceFields import Amber99ForceField
import MMTK.Database

L = 53.86
volume=L**3

universe = CubicPeriodicUniverse(L*Units.Ang, \
     Amber99ForceField(lj_options=12*Units.Ang))

config = PDBConfiguration('fluorine.pdb')


# MMTK can find the database in general:
print MMTK.Atom("F")

# but not when we want create objects from PDBConfiguration
config.createAll()|

*****************************************************************

I get the following traceback

|
/usr/bin/python makePDBuniverse.py
Atom fluorine
Traceback (most recent call last):
   File "makePDBuniverse.py", line 21, in <module>
     a = config.createAll()
   File 
"/usr/people/vyalov/local/lib/python2.6/site-packages/MMTK/PDB.py", line 
428, in createAll
     molecules = self.createMolecules(molecule_names, permit_undefined)
   File 
"/usr/people/vyalov/local/lib/python2.6/site-packages/MMTK/PDB.py", line 
379, in createMolecules
     a = ChemicalObjects.Atom(element, name = aname)
   File 
"/usr/people/vyalov/local/lib/python2.6/site-packages/MMTK/ChemicalObjects.py", 
line 529, in __init__
     ChemicalObject.__init__(self, atom_spec, _memo)
   File 
"/usr/people/vyalov/local/lib/python2.6/site-packages/MMTK/ChemicalObjects.py", 
line 34, in __init__
     blueprint = self.blueprintclass(blueprint)
   File 
"/usr/people/vyalov/local/lib/python2.6/site-packages/MMTK/Database.py", 
line 448, in __init__
     BlueprintObject.__init__(self, type, atom_types, memo)
   File 
"/usr/people/vyalov/local/lib/python2.6/site-packages/MMTK/Database.py", 
line 423, in __init__
     original = database.findType(original)
   File 
"/usr/people/vyalov/local/lib/python2.6/site-packages/MMTK/Database.py", 
line 90, in findType
     filename = databasePath(name, self.directory, False)
   File 
"/usr/people/vyalov/local/lib/python2.6/site-packages/MMTK/Database.py", 
line 58, in databasePath
     raise IOError("Database entry %s/%s not found" % (directory, filename))
IOError: Database entry Atoms/f  not found

shell returned 1 |


*********************************************************************************************
The PDB file looks like this:


|ATOM      1 F            0      18.459  26.301  39.652  1.00  
1.00         F   0.0000
ATOM      2 F            0      30.495  15.275  21.179  1.00  
1.00         F   0.0000
ATOM      3 F            0      18.702  45.771  11.991  1.00  
1.00         F   0.0000
ATOM      4 F            0       9.142  43.718  48.240  1.00  
1.00         F   0.0000
ATOM      5 F            0      48.026  34.727  30.959  1.00  
1.00         F   0.0000
ATOM      6 F            0      16.627  23.149   9.484  1.00  
1.00         F   0.0000
ATOM      7 F            0       5.848  28.479  31.704  1.00  
1.00         F   0.0000
ATOM      8 F            0      26.702  12.069   4.357  1.00  
1.00         F   0.0000
ATOM      9 F            0      35.755  21.043  46.845  1.00  
1.00         F   0.0000
ATOM     10 F            0       8.523  46.952  40.823  1.00  
1.00         F   0.0000|


thanks!



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