AMBER: Tutorial 2: Production MD.

From: a a <>
Date: Wed, 21 Jun 2006 18:19:05 +0800

Dear All,

I am trying to use dynamics simultations to estimate binding energetics for
a drug-protein complex, as it is shown in Tutorial 2.

I use the same file:

Production MD
  imin=0, irest=1, ntx=5,
  nstlim=1000, dt=0.001, ntc=1,
  ntpr=20, ntwx=20,
  cut=16, ntb=0, igb=1,
  ntt=3, gamma_ln=1.0,
  tempi=300.0, temp0=300.0,

After the calculations, I found all the Etot, EKtot, EPtot are positive in
value for drug, protein and the complex, does it means that all the
structures that I have is unstable? What should I do to get a more stable

By the way, how can I extract the best structure after the product MD run in
pdb format.

Please kindly help?

Best regards,

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Received on Sun Jun 25 2006 - 06:07:05 PDT
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