ff96 "favors" beta sheets, but this means that it has an inaccurate energy
and
therefore likely does not describe properties well. It also has what seems
to
be a very poor description of glycine. In general I would not recommend
ff96.
in my opinion you should not choose a force field that is incorrectly
stabilizing
a particular secondary structure just because that's what you want to get
out
of the simulation. it's like telling it what you want the answer to be- when
you
get that answer, how will you know if anything else in the simulation is
incorrect?
just my opinion.
CS
On Nov 5, 2007 12:19 PM, cgji <cgji.itcc.nju.edu.cn> wrote:
> Dr. Carlos's discuss on choosing force field is wonderful .
>
> As mentioned in his discussion, "
> ff03 appears to slightly favor alpha helices ".
>
> Is there a force field favor beta sheet ?
>
> If I want a force field favor beta sheet , could you please give me some
> suggestions on modifying the current parameters .?
>
>
> Many thanks.
>
> 2007-11-06
> ------------------------------
> cgji
> ------------------------------
> *发件人：* Carlos Simmerling
> *发送时间：* 2007-10-17 22:09:52
> *收件人：* amber.scripps.edu
> *抄送：*
> *主题：* Re: AMBER: AMBER 9 - Force Field Options - Question
> 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://structbio.vanderbilt.edu/archives/amber-archive/2007/0663.php -<http://structbio.vanderbilt.edu/archives/amber-archive/2007/0663.php%C2%A0->
> > Suggests using ff99SB for proteins
> >
> > http://structbio.vanderbilt.edu/archives/amber-archive/2001/0264.php -<http://structbio.vanderbilt.edu/archives/amber-archive/2001/0264.php%C2%A0->
> > 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 Wed Nov 07 2007 - 06:07:26 PST
