From: Karteek Bejagam (karteek4_at_vt.edu)
Date: Wed Mar 27 2019 - 00:46:45 CDT
You can use RMSD as a constraint on each protein and use distance as a
reaction coordinate to determine the free energy. RMSD of folded structure
would be smaller than the unfolded one with respect to folded structure.
For the reference structure in colvars, you should consider folded
On Wed, Mar 27, 2019, 1:31 AM Monika Madhavi <monikamadhavi_at_gmail.com>
> Dear all,
> I have a system of two protein molecules (same type). I wand to move one
> molecule while keeping the other molecule fixed and calculate the
> interaction energy between the two molecules with relative position.
> First, I added harmonic restraints to the backbone atoms of the molecule I
> wanted to fix. Then I applied a constant force to all the atoms of the
> other molecule and moved it in the direction I wanted.
> However, I observed that, as the molecule moves, the protein starts to
> unfold. I don't want this to happen. I want to only translate the molecule
> without letting it unfold. If any of you can give some suggestions, that is
> greatly appreciated.
> Thank you.
> Best regards,
> W.A.Monika Madhavi
> Lecturer (Probation),
> Department of Physics,
> University of Colombo.
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