From: Jason Swails <>
Date: Tue, 20 Dec 2011 23:11:15 -0500

On Tue, Dec 20, 2011 at 8:31 PM, Toshifumi Yui <>wrote:

> Dear Jason
> Thank you for your reply.
> Please allow me get things straight.
> For correct delta GB binding calculations (igb = 2), another topology file
> with the modified GB radii should be built by using "set default PBradii
> mbondi2" command.
> For correct delta PB binding ones (ipb = 1), an original topology file with
> a set of default GB radii can be used.

I'm actually not sure what the PB folks use for their calculations. Does
it say somewhere in the manual?

> As regards sleap problem, unfortunately, my actual system is a
> protein-sugar
> complex so that topology files with hybrid 1-4 scaling factors, only
> obtained by sleap, are required for dynamics calculations.

This is actually not correct anymore. A fully patched version of
AmberTools 1.5 has a version of tleap that generates topology files with
variable 1-4 scaling.

> On the other hand, 1-4 interactions should be cancelled out on calculation
> delta G. Use of topology files with common 1-4 scalings will cause no
> effect
> on delta G ?

You are correct for a single-trajectory approach. This is often overlooked
;). Still, though, I would suggest upgrading to the most recent
(fully-patched) version of AmberTools 1.5 in order to take advantage of
"proper" variable-1-4 scaling using tleap.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Dec 20 2011 - 20:30:02 PST
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