AMBER: MM_PBSA GB parameters

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Date: Thu, 25 Mar 2004 10:54:59 +0000

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I would like to carry out an mm_pbsa binding energy analysis, and use=
 identical parameters in a sander implicit solvent MD simulation. I am=
 slightly confused by the gammaG and betaG parameters in=
 '', which seem to correspond to SURFTEN and OFFSET in=
 sander input.=20

In the sander input files generated by, SURFTEN is always set to=
 1.0, and OFFSET to 0.09, regardless of the mm_pbsa input. Then gammaG is=
 set to SURFTEN from the mm_pbsa input, and betaG to SURFOFF from the=
 mm_pbsa input, and these values used to calculate the actual output energy.

It's very likely that I've misunderstood some of this, so please put me=
 straight, but I would like to understand:

Why the variables are passed in this way? - the output offset value =3D=
 0.09 * gammaG + SURFOFF, as far as I can see (though I might be wrong).

What the 'recommended' input values are to mm_pbsa? (and what work this is=
 based on.) The defaults apparently different from the GB in sander. I=
 understand that there is no 'correct' set of values, but if someone more=
 knowledgable than me could explain why things are setup how they are, that=
 would be very helpful.

How can I best modify sander input and/or the mm_pbsa script so the force=
 field used is consistent?


Dave Evans
London School of Pharmacy
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Received on Thu Mar 25 2004 - 11:53:00 PST
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