I think this is not a good idea. ff99SB for nucleic acids is the same as
ff99 (SB only changed proteins), and ff99 had problems that are well
documented in the literature. the force field to use for nucleic acids (in
my opinion) is the bsc0 modification to ff99SB. In my protein-DNA work I use
ff99SB for proteins and bsc0 for nucleic acids.
I would NOT mix ff03 and ff99SB, they are different charge models and nobody
has validated the combination. besides, since ff99SB performs better for
proteins in most comparisons, there is no need to mix ff03 charges with
those in ff94/99/99SB, which are all the same for charges.
On Mon, Mar 22, 2010 at 9:08 AM, mattia <mori.dott.gmail.com> wrote:
> Hi,
> For sure you have to minimize the protein structure (and the solvent, if
> present), before to attempt MD simulations.
> For a similar system (protein-DNA) I've succesfully used ff99SB for nucleic
> acids and ff03 for the protein, modified with Zn-binding parameters [Mori M
> et al., J Chem Inf Model. 2010 Mar 4. (Epub ahead of print)]. Just load both
> of them in leap module.
> About the version of Amber, I've used without problems AMBER10. I think
> the MMPBSA test problem has been already fixed, check the archive.
> However Amber9 should also works fine.
> Regards
>
> Mattia
>
>
>
>
>
> geyan ha scritto:
>
> Hi all amber users,
>> I want to do MD about a system of proteins and DNA complex. Before the
>> MD,I think the first step is to minimize the protein 3D structure which is
>> produced by homology modelling.
>> My question is choosing which force field for protein,which one for
>> DNA, and which one for the complex?all using ff99SB?
>> By the way,amber9 and amber10,which one is better?I have heard of many
>> unexpected problems for amber10 and I met one in MM_PBSA test
>>
>> --------------
>> geyan
>> 2010-03-22
>>
>>
>>
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>
>
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Received on Mon Mar 22 2010 - 07:30:03 PDT
