On Wed, Apr 25, 2012, 本人 wrote:
> Thanks for your advice, especially the website you tell me. however, my
> problem still exists, because my non-standard nucleotide was connected
> to adjacent nucleotides, which means that this nucleotide cannot
> dealed with anchamber, for antechamber provides an automated method
> for creating non-standard units. However, it only works with complete
> molecules, not fragments as I have here. so what I am deeply confused is
> that the two different force fields , Do you mean I must use the only
> one force field (Amber99SB) here, for GAFF was only used for standalone
> molecular, and in other words "I can indeed mix GAFF and Amber99SB
> i.e. 2 different force fields ONLY when I have for instance a ligand
> and a protein i.e. NO CONNECTION between the ligand and the protein.
> and when I have a connection between two different parts I have to use
> the same force field" , am I right? But I don't know how to do it? can
> you tell me in detail? Following your advice, when I added the missing
> terms to the frcmod file, FATAL error happenned, which may de due to the
> mixtion of two force field I used.
This question was already asked and answered just two days ago:
http://archive.ambermd.org/201204/0631.html
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...dac
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Received on Wed Apr 25 2012 - 06:00:04 PDT
