RMSD difference on alignment of two states of protein in VMD and NAMD TMD

From: Nikita chopra (chopranikita.2_at_gmail.com)
Date: Thu Aug 02 2012 - 15:27:36 CDT

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Hi everyone

I am doing TMD of a protein driving the protein from its Inactive to its
target Active conformation. Both are equilibrated structures in water box.
The two conformations differ majorly in its Activation loop conformation.
Therefore, I have used a force constant of value 2 kcal/mol/A(-2) on the
heavy atoms of the Activation loop.On aligning the two states in VMD, the
RMSD value is 7 whereas in TMD setup the RMSD value is shown to be 29. My
Question is:

Does VMD and TMD perform alignment of the two states in a different manner
due to which I see the difference in RMSD in VMD and NAMD TMD ?

I will be grateful for any help in this regard.

Thanks,
Nikita

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