Dear Jason,
The reference energy values calculated for amino acids in CpHMD i.e Aspartate
refene2 = _ReferenceEnergy(igb1=21.4298008, igb2=26.8894581, igb5=26.5980488,
igb7=23.4181107, igb8=26.3448911)
refene2.solvent_energies(igb2=33.2613028)
refene2.dielc2_energies(igb2=12.676908, igb5=13.084913)
refene2.dielc2.solvent_energies()
refene2.set_pKa(4.0, deprotonated=False)
was carboxyl proton on syn- or -anti position ? Do we need to calculate for both positions and average it out as there is only one value for particular IGB model ? Also can you please explain in little more detail the refene2.solvent_energies . I remember you mentioned before that same IGB model is used but with explicit dynamics. I’m not really clear on this part.
Lastly, I see you also calculated the reference energies at int dielec 2. Why is that?
Thanks,
Arsh
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Received on Wed Sep 16 2015 - 08:00:05 PDT
