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Hi,=20
Partially answering my own question, reading Gohlke and Case, J. Comput=
Chem 25:238-250 (2004) (particularly pg.241) makes things clearer. I'm=
sorry for the clueless nature of the previous post.=20
I'm still not sure why offset is set equal to 0.09 (rather than 0) for=
igb=3D1 or 2 when creating the sander input files, though.
Dave Evans
London School of Pharmacy
---- Message from david.evans.ulsop.ac.uk at 2004-03-25 10:54:59 ------
>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.=20
>
>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 =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?
>
>Thanks
>
>Dave Evans
>London School of Pharmacy
>
>
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Received on Thu Mar 25 2004 - 16:53:00 PST
