AMBER Archive (2004)

Subject: Re: AMBER: Test Calculation of atomic charges (RESP) for RNA bases

From: Piotr Cieplak (cieplak_at_cgl.ucsf.edu)
Date: Fri Sep 10 2004 - 12:28:25 CDT

Hi Vlad
Yes, you are right there are some discrepancies in the charge fitting
using the very old (pre 1994) and current RED approach. Previously
it was quite an effort to run geometry optimization on the whole
nucleotides now it is much easier to do so.
Anyway, now we trust more the multi reorientational approach to get charges.
I don't know what is RN-6r category in your tables but apparently
one can see some convergence when going from single RN type charge fit
to RN-6r and Multi-RN approaches. And this would be probably a way to go.
And charges in AMBER - yes with current technology we can think
about changing/improving them a little more, but it would also require
retesting of other properties in MM and most probably adjusting dihedral
parameters.
Piotr
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