Thanks for suggestion Jiri.
>
> 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
>>>>
>>>> ______________________________________________________________________
>>>> 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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>>>>
>>>> _______________________________________________
>>> AMBER mailing list
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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
>>
>>_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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
Received on Mon Feb 04 2013 - 08:30:04 PST
