On Tue, Feb 07, 2012, Hirdesh Kumar wrote:
> I am trying to prepare my protein in tleap. I loaded the protein, solvated
> it with TIP3PBOX water type and now I am trying to neutralize the charge
> with Na+ counter ions. But the added charges are in close vicinity of the
> protein structure and I am afraid that it may affect simulation. I am using
> following command for adding counter ions
> *addIons var Na+ 0*
This should work, and is what is commonly done. Don't forget that you need
lots of equilibration of the solvent before proceeding with a "production"
calculation to be analzyed. The purpose of the equilibration is to reduce the
dependence on details of the starting structure.
You might also look at the "randomizeions" command in ptraj.
....dac
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Received on Tue Feb 07 2012 - 05:00:04 PST
