Dear Asmita,
> There is a file called all_prot_nucleic10.lib which is provided in
> /amber12/dat/leap/lib folder. The file actually has partial charge values
> for protonated nucleic acid bases. My doubt is whether this library could
> be used with recent ff12SB force field for a structure which has both
> standard and protonated nucleic acid bases. And if we can use it, why do we
> need to do a separate Gaussian geometry optimization followed by MEP
> calculation for protonated bases.
if this FF library file contains what you need Yes you can use/test it
with the FF of your choice.
in general one derives charges and build FF library(ies) only for new
molecule(s)/fragment(s).
regards, Francois
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Received on Thu Jun 28 2012 - 00:00:03 PDT
