AMBER Archive (2007)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed Feb 14 2007 - 08:08:17 CST

yes you should be careful of balance. That is why I said I was not aware of
ff03 force field for DNA- the charge model differs from ff94/99/99SB and
may or may not work well. I don't think it has been studied in detail.
we have published several articles on protein/DNA interactions using ff99SB.
Others like Tom Cheatham know the situation with the DNA force field
better, but the charge model is the same for ff99SB and ff94/99 so in
principle it is balanced. However, these do differ in some dihedral terms
for
proteins and for DNA so you'll need to get feedback on that. I am pretty
confident
that ff99SB is better for proteins than ff94 or ff99 (really bad), but I
am less sure of which is better for DNA.

On 2/14/07, Rafi Ahmad <Rafi.Ahmad_at_fagmed.uit.no> wrote:
>
> 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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> Behalf Of *Carlos Simmerling
> *Sent:* 14. februar 2007 13:28
> *To:* amber_at_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_at_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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