Re: AMBER: size of solventbox

From: Germán Sciaini <>
Date: Wed, 23 Feb 2005 07:50:39 -0300

You have to define Ca++ by using of tleap and atom types command. Have a
look if Ca++ is or not included in the amber default parameters....


At 04:07 a.m. 23/02/2005, you wrote:
>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
>Yahoo! India Matrimony: Find your life partner online
>Go to:
>The AMBER Mail Reflector
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Received on Wed Feb 23 2005 - 11:53:02 PST
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