[MMTK] forwarded message from mfpasi at gmail.com

Konrad Hinsen research at khinsen.fastmail.net
Thu Feb 2 08:23:01 UTC 2012


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From: mmtk-bounces at starship.python.net
To: mmtk-owner at starship.python.net
Subject: Auto-discard notification
Date: Thu, 02 Feb 2012 01:12:46 +0000

The attached message has been automatically discarded.
From: Marco Pasi <mfpasi at gmail.com>
To: Ivan Vyalov <vyalov at mis.mpg.de>
Cc: mmtk at starship.python.net
Subject: Re: [MMTK] adding pdb file to universe
Date: Thu, 2 Feb 2012 02:06:01 +0100

Dear Ivan,

I believe the problem is in your PDB.  Looking at the one pasted in
your mail, I think the atom name field should be right-justified (i.e.
in the case of F, two spaces between atom serial number and atom
name).  Furthermore, the residue numbering should change to have one
atom per residue.  Finally, for the compliance freaks, the ATOM record
should be used only for standard amino acids and nucleotides (see
http://www.wwpdb.org/documentation/format33/sect9.html#ATOM): for
other coordinates you should use the HETATM record type (although MMTK
will accept even the ATOM record).

Hope this helps,

Marco

On Wed, Feb 1, 2012 at 5:02 PM, Ivan Vyalov <vyalov at mis.mpg.de> wrote:
> 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!
>
>
>
>
> _______________________________________________
> mmtk maillist  -  mmtk at starship.python.net
> http://starship.python.net/mailman/listinfo/mmtk
>



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Marco Pasi, PhD
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