Hello,
You can add a few ions manually or use genbox. However, it's probably better
to use a vacuum force field and have your peptide uncharged for vacuum
simulations. Any ions you add will have a very strong interaction with the
peptide.
I assume you have a good reason to simulate in vacuo - the mailing list
archives give many reasons why it's not advised.
Ran.
On Sat, 24 Nov 2007 19:47:43 +0200
"OZGE ENGIN" <[EMAIL PROTECTED]> wrote:
Hi all,
I am performing a simulation in vacuum. The peptide has nonzero charge,
so I attempted to neutralize the total charge via genion;however as it is
known, it asks for a continuous group for replacing, but I have no solvent
molecules for the replacement.
How can I neutralize the total charge while performing simulations in
vacuum?
Thanks in advance
Oz.
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Institute of Biochemistry
University of Zurich
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CH-8057 Zurich, Switzerland
Tel. +41-44-6354493
Skype: ran.friedman
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