Re: [AMBER] [Amber] Calculating Normal Modes with Restrictions

From: David A Case <>
Date: Tue, 22 Nov 2016 08:11:35 -0500

On Mon, Nov 21, 2016, The Cromicus Productions wrote:
> I'm currently working with NMA in nab. I can simulate the modes
> and get the frequencies with the code below. I'm working with DNA.
> Say I want to pin both extremes (residues 1,10,11 and 20 for example)
> for my NMA to see "perfect wave" motions, is this possible? What should
> I modify to the code?

One idea: modify your prmtop file to make the masses of the end residues very
large. The recompute the normal modes. The atoms at the end will not move
very much.


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Received on Tue Nov 22 2016 - 05:30:02 PST
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