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