Hi,
I think this is really true for a general system.
In my case I introduced custom zinc binding residues, whose atom point
charges were calculated with a DFT approach. This is the reason for the
usage of ff03 instead of ff99SB for the protein side. However the system
was working finely.
cheers
Mattia
Carlos Simmerling ha scritto:
> 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 - 08:30:03 PDT
