Yes, the first a/g flip may occur during equilibration without bsc0,
you never know in advance. If you have 1-2 flips, it looks visually
stable but is already compromised.
There are real a/g substates in prot/DNA X-ray structures (see papers by
Hartman, e.g.,) but this are not the same as those artifactual
ones produced by pre-bsc0 force fields.
Jiri
On Mon, 4 Feb 2013, Sangita Kachhap wrote:
> Date: Mon, 4 Feb 2013 20:51:58 +0530 (IST)
> From: Sangita Kachhap <sangita.imtech.res.in>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB
>
> Thanks for reply.
> Earlier I did MD simulation of protein-DNA complex & DNA alone for 30 ns and I
> got stable trajectory actualy that time I hadnt any idea about parmbsc0.
> Now I am doing MD simulation of another protein-DNA complex should I use
> parmbsc0? Though for DNA alnoe now I have used it along with ff99SB.
>
>
>> parmbsc0 is the only ff Cornell et al variant that gives stable DNA
>> trajectories, so, it is essential for DNA.
>> It combines well with ff99SB for the protein part.
>> Jiri
>>
>>
>>
>> On Mon, 4 Feb 2013, Sangita Kachhap wrote:
>>
>>> Date: Mon, 4 Feb 2013 18:09:14 +0530 (IST)
>>> From: Sangita Kachhap <sangita.imtech.res.in>
>>> Reply-To: AMBER Mailing List <amber.ambermd.org>
>>> To: amber.ambermd.org
>>> Subject: [AMBER] use of parmbsc0 for protein-DNA complex along with ff99SB
>>>
>>> Hello All,
>>> I have a small query regadring force field. parmbsc0 is modified force filed
>>> of
>>> ff99 for DNA and it is used with ff99SB for MD simulation of DNA.
>>> Since irreversible α/γ transitions from the canonical to a non-canonical
>>> sub-state, accompanied by severe distortions of the structure associated with
>>> ff99 thus to remove this it was modeify to parmbsc0.
>>>
>>> So I have one query should I use parmbsc0 along with ff99SB when doing MD
>>> simulation of protein-DNA complex?
>>>
>>>
>>> With regards
>>> Sangita Kachhap
>>> SRF
>>> BIC,IMTECH
>>> CHANDIGARH
>>>
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>
>
> Sangita Kachhap
> SRF
> BIC,IMTECH
> CHANDIGARH
>
> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
> पिन कोड/PIN CODE :160036
> दूरभाष/EPABX :0172 6665 201-202
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon Feb 04 2013 - 08:00:04 PST
