well my opinion is that one really needs the bsc0 force field for DNA. it is
well documented that other Amber variants do not behave well for DNA- you
say it is working fine, but I would expect that these are either short runs
or you have not yet noticed the problem. I would not recommend this force
field to others, especially when better ones are available.
On Mon, Mar 22, 2010 at 11:04 AM, mattia <mori.dott.gmail.com> wrote:
> 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 - 09:00:04 PDT
