tmd algorithm

From: Elif Ozkirimli (
Date: Tue Feb 10 2009 - 09:22:58 CST


We are trying to use TMD to study the transition of a part of a protein. We
have the equilibrium structures for the open and closed conformations (confA
and confB). The two conformations differ in a certain loop and the rest of
the structure is pretty much the same. Now we would like to push only the
loop from the open to the closed conformation. We assign the value 1 to the
loop occupancy. We have the following questions:

1. How is the alignment performed to start the TMD calculation,
specifically, is the alignment performed on only the targeted (occupancy 1)
loop or the whole structure? Is there a way to specify how to perform the
alignment, eg we want to align everything but the loop.

2. Has anybody used TMD with success in NAMD? If yes, did you use it to
target the whole structure or only a part of the structure?

Thank you very much

Elif Ozkirimli

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