AMBER Archive (2008)

Subject: Re: AMBER: shake the molecule

From: David A. Case (
Date: Fri Oct 03 2008 - 11:28:32 CDT

On Fri, Oct 03, 2008, amit jain wrote:

> I have a system of 10,000 water, 115 Amino acid (5 chain of 23 Amino acid
> sequence) and 5 solute molecule.
> It is desired to SHAKE all the bonded H atom of WATER and all Amino acids.
> In addition to that it is require to SHAKE all internal bonds in solute
> molecule.

I don't think the noshakemask capability will help you here, since it is all
or nothing: if an atom appears in the mask, no bonds to it will be shaken.
I don't think it has the ability to be fine-grained enough to shake bonds to
hydrogen but not to other heavy atoms.

What is your reason for wanting to shake all internal bonds in the solute?
Maybe you can achieve the underlying purpose by some other mechanism (e.g.
through restraints).


[Note: I'm not 100% sure of the above, so if someone wants to examine or even
modify the code, feel free to correct these comments.]
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