AMBER Archive (2006)

Subject: AMBER: Tutorial 2: Production MD.

From: a a (patd_2_at_hotmail.com)
Date: Wed Jun 21 2006 - 05:19:05 CDT

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 md2.in file:

Production MD
&cntrl
  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
results?

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

Please kindly help?

Best regards,
aa

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