AMBER: Simulations with GB models

From: Wei Chen <>
Date: Thu, 11 Jan 2007 11:23:15 -0500

Hi, all,

I try to simulate a protein with two peptide chains using Amber8. Due to the
big size of the system, I have to use implicit water. I choosed a General
Born model (igb=2). I set cutoff 15A, salt concentration 0.1M. I also use
SHAKE and set dt 2 fs. First, I minimized the system for 10,000 steps. Then
heat up the system from 0 to 300K in 20ps. In the crystal structure, the two
peptide chains associate with each other by non-covalent interaction.
However, during the heat-up and following production run, two peptide
chains wander apart more and more. Finally, they separate totally in 40ps. I
don't think this is the real. My question is why the two peptide chains
separate when using General Born model. Is there anyway to overcome this
problem to hold two chains together?

Thank you!

Wei Chen

Control Parameters:

molecular dynamics run with implicit water
    imin=0, irest=1, ntx=5,
    nstlim=44500, nmropt=1,
    ntpr=100, ntwx=500, ntwr=500,
    cut=15.0, ntb=0,
    ntr=0, ntt=1, ntp=0,
    igb=2, saltcon=0.1,
    ntc=2, dt=0.002,
#heat up and equilibrium algorithm:
#from steps 0 to 50000: heat the system to 300K
#from steps 50001-200000: leave at 300K
 &wt type='TEMP0', istep1=0,istep2=4500,value1=138.,
            value2=300., /
 &wt type='TEMP0', istep1=4501, istep2=44500, value1=300.0,
            value2=300.0, /

 &wt type='TAUTP', istep1=0, istep2=44500,value1=1.0,
            value2=1.0, /

 &wt type='END' /


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Received on Sun Jan 14 2007 - 06:07:28 PST
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