there is no "correct" answer. it depends on what you want
to simulate and your needs. I suggest looking at published
papers that are successful in the kind of research you are doing
and follow their methods. Simulations with extra points
or polarizability are really for special needs and probably not
yet our recommendation for "everyday" use. United atom force
fields have limitations but can make simulations faster,
especially in implicit solvents. Make sure you understand
what you are getting into before using those, and check to
see how well validated they have been. I suggest either ff03
or ff99SB. Both have been used successfully and we compared
them in our ff99SB paper. Note that the "99" does not mean that the
parameters are older than ff03- it's actually a more recent paper.
ff03 appears to slightly favor alpha helices over ff99SB- but we're
not yet able to tell which is "correct". ff03 has not been shown
to be compatible with the charge model used for nucleic acids
in amber (maybe ok, maybe not), while ff99SB uses the same model
so is fine. ff03 also seems to disfavor positive phi values needed
in turns- again we're not sure how much of a problem this is, but it's
discussed in our ff99SB paper.
I don't recommend using ff99SP.
CS
On 10/16/07, dpandit.brandeis.edu <dpandit.brandeis.edu> wrote:
> Hello AMBER Experts:
> Before I ask my question about force field, I
> would like to inform you that I am relatively new to AMBER and my
> question is pertinent to proteins and I referred the links below. I
> know there are some more discussions on force fields but the
> conclusion was unclear.
>
> Force field Discussions:
>
> http://archive.ambermd.org/200702/0227.html
> Suggests using ff99SB for proteins
>
> http://archive.ambermd.org/200702/0227.html
> Highlights issues with mix-matching force fields
>
> Question:
>
> I understand that force field selection is one of the most important
> decisions a user makes for performing simulation. I understand
> parameters , atom types and charges go hand in hand. However, as a
> user even after reading the references it is not clear to me which
> force field should I select for protein simulations from the options
> below.
>
> frcmod.ff03, frcmod.ff03ua, parm99EP.dat, frcmod.ff02pol.rl,
> frcmod.ff99SB, frcmod.ff99SP
>
> I am confused by the issue. Please help. Also feel free to let me know
> if I missed something or if there are other references available.
> Below I have listed major options from AMBER 9 manual.
>
> Thank you.
> Deepa
>
> Options available from the Manual for proteins
>
> Amber 2003 (Duan et al.) force field
> frcmod.ff03 For proteins: changes to parm99.dat, primarily in the
> phi and psi torsions.
> all_amino03.in Charges and atom types for proteins.
>
> Amber 2003 (Yang et al.) united-atom force field
> frcmod.ff03ua For proteins: changes to parm99.dat, primarily in the
> introduction of new united-atom carbon types and new
> side chain torsions.
> uni_amino03.in Amino acid input for building database
> uni_aminont03.in NH3+ amino acid input for building database.
> uni_aminoct03.in COO- amino acid input for building database.
>
> Amber 2002 polarizable force field, and recent updates
> parm99.dat Force field, for amino acids and some organic molecules;
> can be used with either additive or
> non-additive treatment of electrostatics.
> parm99EP.dat Like parm99.dat, but with "extra-points": off-center
> atomic charges, somewhat like lone-pairs.
> frcmod.ff02pol.r1 Updated torsion parameters for ff02.
> all_amino02.in Amino acid input ...
> all_aminoct02.in COO- amino acid input ...
> all_aminont02.in NH3+ amino acid input ....
>
> all_amino02EP.in Amino acid input ...
> all_aminoct02EP.in COO- amino acid input ...
> all_aminont02EP.in NH3+ amino acid input ....
>
> Amber 1999 (Wang et al.) force field, and recent updates
> parm99.dat Basic force field parameters
> gaff.dat Force field for general organic molecules.
> frcmod.ff99SB "Stony Brook" modification to ff99 backbone torsions
> frcmod.ff99SP "Sorin/Pande" modification to ff99 backbone torsions
>
>
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Received on Sun Oct 21 2007 - 06:07:08 PDT
