On Fri, Apr 14, 2017, Hadeer ELHabashy wrote:
>
> Concerning the system setup of Amber tutorial B3 for the purpose of All
> Atom Structure Prediction and Folding Simulations of a Stable Protein.
> http://ambermd.org/tutorials/basic/tutorial3/
>
> Why did not he check the charge of the system and add suitable counter ions
> to neutralize it before the simulation? I checked the supported
> TC5b_linear.pdb
> <http://ambermd.org/tutorials/basic/tutorial3/files/TC5b_linear.pdb> with
> XLeap and I found that it has a total charge of +1. I am trying to run
> similar simulations on a system that has a total charge of +6. Do you think
> that neutralizing this system or any other system undergoing this type
> of folding
> simulations may affect the results significantly?
The larger the net charge, the more likely it is that neutralization may have
a significant effect. Many people routinely use mobile counterions to
neutralize everything; others may skip it for systems with a fairly small net
charge.
Maybe others on the list have experience of protein folding simulations with
and without counterions, and can report that here.
....dac
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Received on Thu Apr 13 2017 - 19:00:03 PDT
