AMBER Archive (2006)

Subject: Re: AMBER: Which one is the best force field for DNA?

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Fri Apr 14 2006 - 11:41:04 CDT

I haven't done this but would be very worried that the important
electrostatic
interactions such as H-bonding would not be balanced between the two charge
models, even if they do a similar job within a charge model. Protein-protein
H-bonds might have different energy profiles than protein-DNA, thus giving
you a poor overall model. This is basically what Tom C was saying.
carlos

Vlad Cojocaru wrote:

>Hi Tom, Jiri, David, all ambers
>
>Now, what about ff03? According to your opinion, is it recommended to be
>used in protein-nucleic acids complex simulations? Or is it "safer" to
>stick to ff99 for that purpose? It would be interesting if anybody has
>done simulations of protein-RNA or protein-DNA complexes with ff03 and
>compared them to simulations done with ff99..
>
>cheers
>vlad
>
>
>
>Thomas E. Cheatham, III wrote:
>
>
>
>>>Well, I did read sometime ago Tom's review, maybe I missed (or I forgot)
>>>some of the information there so I'll read it again ...So, I didnt know
>>>that ff99 (thus also ff03) doses not include the ff98 changes. Is there
>>>a particular reason why those changes were not included in newer versions?
>>>
>>>
>>>
>>>
>>ff99 does contain a slightly modified set of the ff98 changes; they are
>>not exactly the same (which likely led to DAC's comments), but very
>>similar.
>>
>>In ff98, we adjusted angles related to chi and the sugar in an attempt to
>>improve helical twist (increase it slightly) and to increase chi. This
>>was successfully accomplished, yet, we appeared to lose some of the
>>favorable features of ff94 in relation to stabilization of A-DNA in mixed
>>water/ethanol and with highly charged cations (hexammine cobalt(III)).
>>So, in some sense, one cannot definitely state that ff98 is "better" than
>>ff94, just different in that it has a slightly improved overall helical
>>twist.
>>
>> Cornell ff98 ff99
>>CT-OS-CT-N* V3 1.15 0.383 0.383
>> V2 0.0 1.0 0.65
>>
>>OS-CT-CT-OS V3 0.144 0.144 0.144
>> V2 1.0 1.5 1.175
>>
>>OS-CT-N*-CK V2 0.5 pi 0.0 0.0
>>or CM V1 2.5 2.5 2.5
>>
>>(the "pi" denotes a phase of 180; all other phases are 0 and the numbers
>>shown are the peak heights).
>>
>>
>>
>>
>>
>>>If I may, as a short comment on this, I believe that it is important to
>>>be able to use the same ff for both proteins and nucleic acids (perhaps
>>>membranes also) as they do coexist and many simulations involve
>>>
>>>
>>>
>>>
>>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. However, with respect to the ff94->ff99, the only
>>differences are largely dihedral parameters and not the overall
>>philosophy. Equivalent methods were used to generate charges, van der
>>Waals parameters such that all of these variants are compatible. This is
>>not true when comparing ff94->ff99 with the polarizable ff02 or ff02EP or
>>the new charge derivation philosophy of ff03 where there could
>>be-- although this has not been shown to my knowledge-- misbalance.
>>
>>--tom
>>
>>\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
>>-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
>>/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
>>\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
>>-/-
>>/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
>>\-/ BPRP295A http://www.chpc.utah.edu/~cheatham
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>>
>
>
>

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