AMBER Archive (2005)

Subject: Re: AMBER: size of solventbox

From: Germán Sciaini (gsciaini_at_qi.fcen.uba.ar)
Date: Wed Feb 23 2005 - 04:50:39 CST

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....

G.

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
>results?
>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?
>
>Thanks in advance
>
>
>=====
>===========================================================================
>
>/\/\athew
>
>Mathew K Varghese
>Research Scholar
>School of Pure and Applied Physics
>M.G.University
>Kottayam, Kerala
>India
>
>email mathew_kvarghese_at_yahoo.co.in
>
>===========================================================================
>
>________________________________________________________________________
>Yahoo! India Matrimony: Find your life partner online
>Go to: http://yahoo.shaadi.com/india-matrimony
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu