When you wish to fold a protein, you require that the RMSd be high
eventually. Additionally if you are simulating a long chain in vacuum,
you can expect RMSd to start accumulating immediately.
I am not sure what tutorial you are looking at. You may want to do some
general research on protein folding if you haven't, because vacuum
folding is not a method in practical use that I have heard. You may want
to consider a Born solvent approximation as a minimal step up in any
case. It is so quick to run these calcs it would almost be foolish to
avoid them, since they get one off to an inspiring start.
Bill
On 8/17/16 10:50 PM, Wong Li Zhe wrote:
> Thanks for the reply.
>
> With MD simulation, we hoping to fold the long chain of the protein before proceeding with screening the protein model with compounds.
>
> Any input whether the high angstroms value is OK in this case?
>
>
> Thank in advance.
>
>
> Best regards,
>
> Li Zhe
>
> ________________________________
> From: Wong Li Zhe <Wong.LiZhe.student.imu.edu.my>
> Sent: Thursday, 18 August, 2016 12:12:52 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] RMSd
>
> Hi.
>
>
> We are just trying to fold the long chains of this protein.
>
>
> Best regards,
>
> Li Zhe
>
> ________________________________
> From: Hai Nguyen <nhai.qn.gmail.com>
> Sent: Thursday, 18 August, 2016 12:11:05 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] RMSd
>
> hi
>
> What do you want to learn from this type of simulation?
>
> Hai
>
> On Thu, Aug 18, 2016 at 12:08 AM, Wong Li Zhe <Wong.LiZhe.student.imu.edu.my
>> wrote:
>> Dear AMBER users,
>>
>>
>> I am currently simulating a protein (1304 amino acids) in vacuo without
>> restraints.
>>
>> >From the RMSd versus time plot, the RMSd is about 140 angstroms!
>>
>> I wonder is this observation still consider as normal?
>>
>> As from the tutorial, this is considered as 'blown up'.
>>
>> Any inputs will be much appreciated.
>>
>>
>> Thank you.
>>
>>
>> Best regards,
>>
>> Li Zhe
>>
>>
>> [http://imu.edu.my/e-banner/openday-sep-2016.jpg]
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>> Come visit us at the September Open/Info Days!
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Received on Wed Aug 17 2016 - 23:30:03 PDT
