Re: [AMBER] internal geometry restraint

From: Jason Swails <>
Date: Tue, 26 Nov 2013 11:31:35 -0500

On Tue, Nov 26, 2013 at 11:06 AM, Jio M <> wrote:

> Dear All
> I have three linear polymers and I have placed them parallel to each
> other. I am not sure they have been placed 'very close' because my script
> just considered the atoms as point coordinates while placing them. So when
> I run a simulation they are repelled to each other in just 50 ps and the
> internal geometry of each polymer chain is destroyed badly.
> What I am thinking is to run first some simulation considering three
> polymer chains as 'hard rods', that is keeping internal geometry
> coordinates of a polymer constrained (all atoms in a polymer chain being
> fixed with respect to each other; keeping internal geometry of polymer
> chain fixed) so that they just act as hard rods and can adjust their
> positions and later I release the restraints.
> I know the positional restraints that we can keep the whole structure
> fixed like (with ntr =1 ). In above case which flag is to be used? NMR
> restraints is a good idea or something simple?

NMR restraints are basically your only option for restraining internal
degrees of freedom without imposing the (very restrictive) positional
restraints to do the same thing. You will obviously need to use lots of
NMR restraints to accomplish what you want to do, but with a bit of
scripting it is feasible.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Nov 26 2013 - 09:00:02 PST
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