Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"

From: David A Case <>
Date: Mon, 30 Sep 2013 08:01:34 -0400

On Mon, Sep 30, 2013, 冉挺 wrote:

> I read the tutorial that's "Thermodynamic Integration using soft core
> potentials

> I want to modeling the water contribution to the ligand-binding affinity by
> the double decoupling method.

It's not clear what you mean by the "water contribution to the ligand binding
affinity". A "standard" simulation of the ligand binding free energy will
automatically include the effects of the solvent.

> I wonder if the icfe parameter should be set from minimization
> mdin to equilibrium mdin

You would ordinarily use the same icfe value at all steps. Note that
minimization is often not needed.

> if the water should be constraint at the
> binding site by a constraint force as described in the literature

You would ordinarily not constraint solvent molecules. But note that it may
take a long time to equilibrate if there are trapped waters.

> As well, I cannot use the pmemd method to run Thermodynamic Integration

This is correct; the next release of pmemd will have this feature.

> My command is "sander -ng 2 -groupfiles 《Mygroupfiles》"
> the erro is "mdfil: Error unknown flag: -ng" but the recommended
> parameters include the -ng flag. I used amber10.

You must use sander.MPI (not sander), and the corresponding mpirun command to
carry out thermodynamic integration calculations.

Since you seem to be very new to this, be sure to get familiar with small and
"easy" transformations before attempting something difficult.

...good luck...dac

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Received on Mon Sep 30 2013 - 05:30:04 PDT
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