Homa Azizian wrote:
Hi
I have a basic question about the charge. why is it important to neutralize
the charge of ligand-protein complex. Is it true by neutralizing the tatal
charge of ligand-protein complex we prevent the electrostatic intraction of
ligand and protein?
Any suggestion would be appreciated.
Physical systems are normally neutral - cells have to do work to
maintain ion and/or charge imbalances.
Physical models were normally parameterized under neutral conditions -
but you should check the literature for your force field.
Some algorithms might be doubtful under non-neutral conditions - I'm not
sure whether Ewald methods are well-formed in such cases. Most
derivations I've seen seem to require it.
Mark
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