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
>>
>> ______________________________________________________________________
>> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
>> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
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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
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Received on Mon Feb 04 2013 - 07:30:03 PST
