Ran Friedman, Biochemisches Inst. wrote:
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.
It is not advised as a model for peptides in solution, but if you want
to model something in vacuo then it is fine. In that case you may want
to look for evidence of the charge of the peptide in vacuo from mass
spec experiments.
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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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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