AMBER Archive (2005)

Subject: AMBER: size of solventbox

From: mathew k varghese (mathew_kvarghese_at_yahoo.co.in)
Date: Tue Feb 22 2005 - 22:07:00 CST

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