AMBER Archive (2009)

Subject: Re: [AMBER] Can bonded pair of atoms be restrainted by NMR distance restraint?

From: David A. Case (
Date: Sun Feb 01 2009 - 12:35:03 CST

On Sun, Feb 01, 2009, liu junjun wrote:

> ======= NMR distance restraint file ====
> &rst IRESID=0, iat=8385,8384, r3=3.04,
> r4=3.1, r1=3.04, r2=3.04, rk2=8000, rk3=8000,/
> &end

When r1=r2, there is no restraint at all for distances less than 3.04
Ang. Also, since r3 is so close to r4, there is only a very weak
restraint on distance greater than 3.04 Ang.

You should actually plot out the restraint energy as a function of
distance to see what is happening. Based on what you wrote, you
probably want r1 to be quite small, and r4 to be quite big.


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