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 - 22:30:02 PST
