AMBER Archive (2004)

Subject: AMBER: MM_PBSA GB parameters

From: david.evans_at_ulsop.ac.uk
Date: Thu Mar 25 2004 - 04:54:59 CST

Hi,

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 'mm_pbsa_statistics.pm', which seem to correspond to SURFTEN and OFFSET in sander input.

In the sander input files generated by mm_pbsa.pl, 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 = 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?

Thanks

Dave Evans
London School of Pharmacy


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