Dear All,
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*
I also tried with addIons2 but in this case, only 4 Na+ are away from
protein but 8Na+ are still in close vicinity to the protein. Please let me
know how should i neutralize my system effectively.
Thanks and Regards,
Hirdesh Kumar
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Received on Mon Feb 06 2012 - 21:30:04 PST
