RE: AMBER: size of solventbox

From: Ross Walker <>
Date: Tue, 22 Feb 2005 21:22:03 -0800

Dear Mathew,

> I have two questions.
> In the simulation of nucleic acids, to add explicit
> solvent is it necessary to use a solvent box extending
> 9 or 8 Angstroms from the solute? Due to the
> limitations of computational facitities I have used a
> solventbox of 3 Angstroms.How this will affect the
> results?

This will definitely cause artifacts in your simulation. But it is probably
quite hard to quantify. Perhaps some can comment further. There may be some
work published that tries to quantify the effects of the size of the
explicit solvent box but I don't know. Note for PME calculations your cutoff
should be about 8A and this needs to be less than half your smallest box
diameter. Hence the smallest axis of your box needs to be larger than 16

> Second:
> In the pdb data of an RNA there are two calcium atoms
> at one end. How can I add the atomtype of these two
> atoms?

This should give you an idea of how to proceed. You will need to decide
whether or not the ions need to be bound to the RNA or can be free floating.
This will depend on their 'purpose' in the RNA structure.

I hope this helps.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
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Received on Wed Feb 23 2005 - 05:53:00 PST
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