[MMTK] Introducing a new force-constant on a particular residue

Konrad Hinsen research at khinsen.fastmail.net
Mon Aug 12 13:40:56 UTC 2013

Sandhya.Tiwari at mbi.uib.no writes:

 > I am trying to find a way to mimic a perturbation at a given
 > residue position and examining the difference in the fluctuations
 > as a result of this on the structure. I would like to halve the
 > force-constant at this given residue position i, and recalculate
 > the modes accordingly, using the C-alpha forcefield. Has anyone
 > tried this before? Is there a way I could do this and still receive
 > an MMTK modes object, with the fluctuations etc. as an attribute?

If I understand your situation correctly, you want to modify the force
field for a normal mode calculation. What I don't quite understand is
how you want to modify it. Force constants in the CalphaForceField are
defined not per residue, but between pairs of residues. What you can
do is halve the force constants between residue i and all the other
residues, for example.

There is a minor technical problem: you cannot modify individual terms
in the CalphaForceField, which has only two parameters: the cutoff and
a global scale factor. However it is quite straightforward to rewrite
your own version of CalphaForceField in Python, in which you can then
modify whatever you like. See the attached example script for the

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
ORCID: http://orcid.org/0000-0003-0330-9428
Twitter: @khinsen
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