Hi
You can read a series of papers from David Baker lab.
Your system is super big for MD folding.
Hai
> On Jan 18, 2017, at 1:23 AM, Wong Li Zhe <Wong.LiZhe.student.imu.edu.my> wrote:
>
> Thanks for the reply, Hai.
>
> I wonder why Rosetta is a better software here?
>
>
> Best regards,
>
> Li Zhe
>
> ________________________________
> From: Nhai <nhai.qn.gmail.com>
> Sent: Wednesday, 18 January, 2017 11:10:19 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Model Folding
>
> Rosetta seems to be better software here.
>
> Hai
>
>> On Jan 17, 2017, at 9:49 PM, Wong Li Zhe <Wong.LiZhe.student.imu.edu.my> wrote:
>>
>> Dear AMBER users,
>>
>>
>> I am currently on a project where the objective is to design a protein model (1304 amino acids).
>>
>> There are 3 long chains present on the protein model. One of the shorter chains has finally folded and now left with 2 long chains.
>>
>> Restrains were applied on the model letting only 1 long chain to fold at a time.
>>
>> AMBER version 2011 was used throughout the simulation process.
>>
>> The parameter used was:
>>
>> imin = 0,
>> ntb = 0,
>> igb = 0,
>> cut = 10.0,
>> ntr = 1,
>> tempi = 0.0,
>> temp0 = 300.0,
>> ntt = 3,
>> gamma_ln = 1.0,
>> nstlim = 100000,
>> dt = 0.001,
>> ntpr = 100,
>> ntwx = 100,
>> ntwr = 100
>> /
>>
>> I wonder is there a better/quicker way in folding the long chains? As I would need the final model as soon as possible.
>>
>>
>> Thanks in advance.
>>
>>
>> Best regards,
>>
>> Li Zhe
>>
>>
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Received on Tue Jan 17 2017 - 23:00:02 PST
