[AMBER] Model Folding

From: Wong Li Zhe <Wong.LiZhe.student.imu.edu.my>
Date: Wed, 18 Jan 2017 02:49:02 +0000

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 - 19:00:02 PST
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