[MMTK] Normal modes -protein

Mohan maruthi sena maruthi.sena at gmail.com
Tue Dec 11 18:22:44 UTC 2012


Hi all,
            I want to calculate  normal modes for a protein using mmtk.  I
have taken a part of protein ,one residue containing five atoms. In
principle it has 3N degrees of freedom and hence less than 15 frequencies.
I have calculated frequencies as given in the tutorial and I got 35
frequencies. Can anyone please explain how does mmtk calculates frequencies
and why I got 35 frequencies? The pdb and MMTK  commands that I have used
are shown below:

pdb:
ATOM      1  N   ALA A   2      35.783  48.487  14.085  1.00
27.25           N
ATOM      2  CA  ALA A   2      36.957  47.698  13.544  1.00
26.83           C
ATOM      3  C   ALA A   2      38.160  47.994  14.479  1.00
26.43           C
ATOM      4  O   ALA A   2      39.143  48.684  14.282  1.00
26.80           O
ATOM      5  CB  ALA A   2      37.292  47.895  12.115  1.00
26.88           C
END

MMTK commands:

*from* MMTK *import* *

*from* MMTK.Proteins *import* Protein
*from* MMTK.ForceFields *import* Amber94ForceField
*from* MMTK.NormalModes *import* NormalModes


universe = InfiniteUniverse(Amber94ForceField())
universe.protein = Protein('two.pdb')
modes = NormalModes(universe)
*for* mode *in* modes:
    *print* mode

Thanking you in advance,
Mohan
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://starship.python.net/pipermail/mmtk/attachments/20121211/7d90f704/attachment.html>


More information about the mmtk mailing list