AMBER Archive (2009)

Subject: Re: [AMBER] charges in topology file

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Fri Jul 10 2009 - 11:20:01 CDT

Dear AMBER users,

   We are going to study the conformational change of protein between two different states by using TMD methods. I have some confusions about TMD and request your help.

I list my questions as follows:

Suppose we have two conformations for a protein system, titled "A" and "B". I am going to check the conformational change from A to B.

1. Should the initial structure (A state) be equilibrated before starting the TMD simulation? If so, the starting conformation (A' state) in TMD is not the same as the initial conformation (A state). Then does this simulation represent one of the possible the pathways from A to B?

2. How should I solvate the protein, in implicit or explicit waters? I noticed that someone uses the water shell, not a box full of water, to solvate the solute. What the difference between the two choices? Which one should I use?

3. We used the full explicit solvation of protein in the conventional MD for 15 ns. Can I start the TMD simulation from an equilibrated snapshot, e.g. the snapshot at 3 ns?

Thanks so much.
   
Jeffrey

-----------------------------------------------
  
  State Key Lab. of Molecular Reaction Dynamics(SKLMRD),
  Dalian Institute of Chemical Physics(DICP),
  the Chinese Academy of Sciences(CAS),
  
  Zhongshan Road457, Dalian City,
  Liaoning Province 116023,P. R. China

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