2 domains rigid body rotation with IMD

From: Matteo Cattaneo (teosuck_at_yahoo.com)
Date: Fri Dec 05 2003 - 08:28:22 CST

I have a protein made of two domains (lid domain and
catalitic domain) and I need to rotate one (lid)
respect to the other (catalitic) to reveal the
active site of the enzyme.
I'd like to perform an IMD simulation, with namd and
WMD, where:

-catalitic domain will be kept fixed (with AtomFix)
-backbone's segment connecting the 2 domains is free
to move
-lid domain is moved as a rigid body by a force
applied on each atom (by IMD)

this should simulate a kind of torque making the lid
rotate around the "hinge"
rappresented by the free backbone segment.

I'm performing this simulation on a standard PC and if
the force is applied on
a small number of atoms or residues it seems to work
fine but structuration is lost,
so I need to apply the SAME force (intensity and
direction) on all the atoms of the
lid domain to make it rotate as a rigid body and keep
his structuration (the secondary
structure should be lost only in the free part of the
backbone since catalitic domain
is fixed)

In WMD is possible to apply force by atom, residue or
Is it possible to apply a constant force just on the
backbone's atom of a
range of residues (say from 220 to 390) ?

I've tried also to "cheat" WMD editing the PDB file
and make all the residues I need
to move to appear as one residue: in this way it is
possible to apply the same force
to a big number of atoms in just 1 click but the
calculations become too slow. Again I
need to apply the force only to the backbone. I tried
to edit the PDB making all the CA,
of the residues range I need, to appear as one residue
but namd doesn't like this kind of
Is it possible to define a "fragment" containig only
such a atoms (CA or backbone)?

Any advice on how to rotate a part of a protein
respect to an other as a rigid body will
be appreciated.

Matteo Cattaneo

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