[AMBER] positional restraint to within stipulated distance

From: Eng H Yap <eyap.einstein.yu.edu>
Date: Tue, 30 Oct 2012 03:00:01 +0000


I want to run MD on a ligand (specifically an amino acid), while restricting its C-alpha position to within 2 angstroms from its starting (i.e. reference) position. ntr=1 does not work for me because I cannot impose the distance requirement with the harmonic potential. likewise nmropt=1 with &rst does not work because I want to restraint distance between current vs. reference atoms, not between two current atom positions.

Is there a way to do what I want? I can think of two possible ways
1. if there is a square-well potential for ntr=1, or
2. add a dummy/dimensionless atom with reference position same as the C-alpha, freeze its position with ntr, then use &rst to restraint the C-alpha-to-dummy distance to 2 angstrom. but I am not sure how to create such a dummy atom.

Any suggestion?

Thank you!
Enghui Yap
Albert Einstein College of Medicine

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Received on Mon Oct 29 2012 - 20:30:27 PDT
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