AMBER Archive (2007)

Subject: Re: AMBER: AMBER 9 - Force Field Options - Question

From: dpandit_at_brandeis.edu
Date: Wed Oct 17 2007 - 10:27:12 CDT

Dear Dr. Simmerling:
                     Thank you very much for your detailed reply. I
just want to be sure about the references and options. From the manual
it seems I will use following options in LEap based on my selection

if ff99sb then
topology based on Cornellet al. 1994, parameters - parm99.dat+frcmod.ff99SB

Reference
ff99sb - Proteins. 2006, 65, 712-25. Comparison of multiple Amber
force fields and development of improved protein backbone parameters.

if ff03 then topology based on Duanet al. 2003, parameters -
parm99.dat+frcmod.ff03

Reference
ff03 - Journal of Computational Chemistry, 2003, 24, 1999-2012. A
point-charge force field for molecular mechanics simulations of
proteins based on condensed-phase quantum mechanical calculations.

Please correct me if I am wrong.

Regards,
Deepa

Quoting Carlos Simmerling <carlos.simmerling_at_gmail.com>:

> 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_at_brandeis.edu <dpandit_at_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 -
>> Suggests using ff99SB for proteins
>>
>> http://structbio.vanderbilt.edu/archives/amber-archive/2001/0264.php -
>> 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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