AMBER Archive (2007)

Subject: AMBER: Best Force field for protein, DNA, and organic compounds?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Tue Feb 13 2007 - 22:13:31 CST

Dear Amber Users,

I am new to AMBER, I could like to do a stimulation for a complex with
protein, DNA and organic coactivator. I read from the literature that
para99 is better for DNA stimulation? GAFF is better for organic compounds.
  Is it true that they are the best? Is it also true for protein?

Follow the tutorial 1, I used the command
usr/local/amber8/dat/leap/cmd/leaprc.ff99. Read the xxx.lib and xxx.frcmod
from Antechamber. Does it call for the best force field parameters for
protein, DNA and organic compounds?

If not, what should I do to make use of the best forces field for different
components?

Best regards,

Catherine

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