AMBER Archive (2006)

Subject: Re: AMBER: Tutorial 2: Production MD.

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Wed Jun 21 2006 - 10:37:51 CDT

Dear aa,

as with most tutorials, the input files provided are geared towards short
calculation runs for exemplary results, not useful in actual research.

> 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,
> /

If you want to do an MM-PBSA like approach, your simulation time of 1ps is
much too short! Run your MD simulation for at least a nanosecond (you
might need much more than that, depending on your system) and carefully
check for convergence

> 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?

Those values only mean something when compared to other energies, since
your coice of a zero-point of energy is quite arbitrary. For a quick
estimate of the binding energy you should calculate
E(COM)-[E(REC)+E(LIG)].

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

The ptraj program allows you to transfer trajectories into pdb-files, but
I'm not sure what you mean by the best structure.

Regards,

Thomas
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