[MMTK] Auto-discard notification

Konrad Hinsen research at khinsen.fastmail.net
Fri Apr 9 09:32:07 UTC 2010


On 09.04.2010, at 05:11, mmtk-bounces at starship.python.net wrote:

> but when i used the construct.py  along with water molecules
> 
> #! /usr/bin/python
> from MMTK import *
> from MMTK.PDB import PDBConfiguration
> from MMTK.Proteins import PeptideChain, Protein
> configuration = PDBConfiguration('6LYZ.pdb')
> chains = configuration.createPeptideChains()
> insulin = Protein(chains)
> insulin.writeToFile('bala1.pdb')
> 
> the output file did not contain any water molecules in it. 
> could anyone  suggest how to include waters...

Your script explicitly constructs the protein only, throwing away everything else: solvent, ligands, and nucleic acid chains.

For constructing a more complex system, you will have to start by creating a universe, and then add everything you want. 
The following variant of your script will construct everything in the PDB file:

from MMTK import *
from MMTK.PDB import PDBConfiguration
from MMTK.Proteins import PeptideChain, Protein
configuration = PDBConfiguration('6LYZ.pdb')
universe = InfiniteUniverse()
universe.addObject(configuration.createAll(None, 1))
universe.writeToFile('6LYZ_with_hydrogens.pdb')

You can be more selective, of course.

> Moreover I would like to do MD with the crystallographic water molecules using the periodic boundary conditions. Is this reasonable, hope someone give suggestions.

What exactly do you want to do? Do you want to define a periodic system corresponding to the crystal? In that case, you need to re-create the unit cell contents from the asymmetric unit, which is what is stored in a PDB file. Look at Examples/Miscellaneous/crystal_periodic.py (in the MMTK distribution) for an example. Note however that an MD simulation based on the unit cell contents is very likely to be unstable, since many if not most solvent molecules are invisible in X-ray crystallography. You would be simulating a crystal with holes in it.

But perhaps what you want is to take the protein and crystallographic water from a PDB file, put it into a larger periodic system, and add lots of solvent. In that case, the example script to look at is Examples/MolecularDynamics/solvation.py.

Konrad.
--
---------------------------------------------------------------------
Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
Saint Aubin - BP 48
91192 Gif sur Yvette Cedex, France
Tel. +33-1 69 35 97 15
E-Mail: research at khinsen dot fastmail dot net
---------------------------------------------------------------------










More information about the mmtk mailing list