Chih-Ying Lin wrote:
Hi
I am going to simulate the lysozyme with some ligand in the low ionic
strength phosphate buffer .
The buffer condition will be
(pH 7.2, 8.3 mM) and (pH 5.0 , 8.3 mM)
For the buffer condition (pH 7.2, 8.3 mM), I will use TIP3P water
model and use CL- ions to nutralize the lysozyme (+8)
and cationic ligands.
Does my setting make sense?
It makes sense, but it doesn't model those buffer conditions. Calculate
how many H+ you'd need in your simulation cell for pH 7.2. Likewise the
phosphate species.
Do you have any suggestion about this ?
Consider the titratable residues when trying to model a system at a
different pH.
Mark
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