AMBER: size of solventbox

From: mathew k varghese <>
Date: Wed, 23 Feb 2005 04:07:00 +0000 (GMT)

Dear amber users,

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

Thanks in advance



Mathew K Varghese
Research Scholar
School of Pure and Applied Physics
Kottayam, Kerala



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Received on Wed Feb 23 2005 - 04:53:00 PST
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