(unknown charset) Re: Re: [AMBER] about amber force field

From: (unknown charset) geyan <geyan.big.ac.cn>
Date: Tue, 23 Mar 2010 10:36:44 +0800

thanks for all your reply. It's very helpful.
Also looking forward to the improvements in Amber11.


2010-03-23



geyan



发件人: Carlos Simmerling
发送时间: 2010-03-22 23:38:36
收件人: AMBER Mailing List
抄送:
主题: Re: [AMBER] about amber force field
 
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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>
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Received on Mon Mar 22 2010 - 20:00:02 PDT
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