Re: AMBER: MM_PBSA GB parameters

From: <>
Date: Thu, 25 Mar 2004 16:25:56 +0000

This is a MIME-encapsulated message
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline


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 at 2004-03-25 10:54:59 ------
>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
Content-Type: text/directory; charset="iso-8859-1"; profile="vcard"; name="david_evans.vcf"
Content-Transfer-Encoding: quoted-printable
Content-Disposition: attachment; filename="david_evans.vcf"

PRODID:-//Gordano//NONSGML GMS 9.02.3180//EN
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Mar 25 2004 - 16:53:00 PST
Custom Search