AMBER Archive (2006)

Subject: Re: AMBER: how to create 2'-5' RNA

From: FyD (
Date: Sat Jun 24 2006 - 01:29:43 CDT


> I am attempting to model some 2'-5' RNA molecules (using Amber 8). In leap I
> edited RC, RC5, RG, RG5, etc not to have HO'2 atoms but to have HO'3 atoms. I
> saved these prep files changed them by hand to have the correct charges and
> atom types for O3', O2', C3', C2', and HO'3.

My feeling is that changing _by hand_ charge values has to be banned. There is
nothing scientific/rigorous in manually adapting/cheating charge values.
Moreover, by doing so you have no idea about how your 'adapated' charge values
reflect the MEP.

Instead you have to optimized the right molecule and get the right conformation,
generate the charge values using the right fragment, etc...

regards, Francois

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