Hi Carlos,
I am a bit confused from this reply. I check some of the old posts here
at Amber (Apr-2006) and it was mentioned by couple of folks there that
"As a general rule, you do want consistency between force fields such
that
if you run proteins and nucleic acids or membranes, there is not a
mis-balance."
So by using 2 different ffs as mentioned by you here for DNA and protein
cause a "mis-balance"
Also the following was mentioned by Tom in the same thread
"If I were to do a protein-RNA simulation with what is generally
available
today, I would likely use one of the modified phi/psi protein parameter
sets by the Simmerling group (see the JACS 2002 article on TrpCage
folding); if you have amber9 (or are getting AMBER9), this is the
frcmod.ff99SB"
Do you think that using this ff99SB (developed by your group) be a good
choice for Protein-DNA interaction?
Regards
Rafi
________________________________
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Carlos Simmerling
Sent: 14. februar 2007 13:28
To: amber.scripps.edu
Subject: Re: AMBER: Best Force field for protein, DNA, and organic
compounds?
in my opinion, ff99 for proteins should never be used. use ff99SB or
ff03.
others may suggest what is best for DNA- I think ff94 or ff99 and I do
not think
there is any such thing as ff03 for DNA. others may know more.
On 2/13/07, Catein Catherine <askamber23.hotmail.com> wrote:
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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Received on Sun Feb 18 2007 - 06:07:06 PST
