On 5/2/13 7:33 AM, Mohan maruthi sena wrote:
Hi ,
Thanks for a quick reply. Sorry for not being clear, I want to
surround the peptide with just ions(sodium). How can I do this?
genbox -ci -nmol
You will need a coordinate file for a single Mg2+ ion to be inserted, which is
trivial to create by hand. I don't know how the ion force field parameters will
behave in the absence of explicit solvent. Are you planning to use implicit
solvent?
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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