Re: [AMBER] internal geometry restraint

From: Jio M <>
Date: Tue, 26 Nov 2013 19:09:18 -0800 (PST)

Dear Jason and David

Thanks for reply, I think updated force fields (like ff10) are not implemented in other dynamics programs. Using NMR restraints option seems ok though tiring.
I have two queries:
I have read amber tutorial:

1) For distance restraints only the non-bonded atoms need to be considered ? I think no need to consider bonded atoms. To make work little easier can I get non-bonded atom distances by some command in amber?

2) As I am not heating to higher temperatures can I skip to provide angle restraints? Or I need to try and see? Similarly any command that can print angles (torsions) in my molecule.


kind regards

On Tuesday, November 26, 2013 10:56 PM, case <> wrote:
On Tue, Nov 26, 2013, Jio M wrote:

> 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.

You can carry out a version of this sort of calculation using "EMAP"
constraints, as explained in section 6.13 of the manual.  This is not exactly
what you describe, but it might suffice.  You'll probably have to experiment a
bit (or a lot!) with force constants and the resolution of the maps you are
using.  Some other dynamics programs do a better job of allowing you to define
rigid groups that can move relative to each other.


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Received on Tue Nov 26 2013 - 19:30:02 PST
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