Dear Amber users,
How do I account for the pka shifts of each of the
polarisable amino acids in my protein at a particular
constant pH.
I do not find much of a difference between H++ server generated pdb file
and xleap generated pdb file (i.e in the way Hydrogens have been added)
atleast with respect to my protein.
I have read the threads on this before. But,Can someone please elucidate
more on the concept of accounting for protonation states of each
polarisable amino acid in a protein?
With regards,
Abinaya
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Received on Wed Feb 15 2012 - 04:00:02 PST
