RE: AMBER: PBradii

From: Steve Seibold <>
Date: Tue, 11 Sep 2007 15:21:21 -0400

Ok. Thanks for your explanation and advice Carlos. They were very






From: [] On Behalf
Of Carlos Simmerling
Sent: Tuesday, September 11, 2007 3:07 PM
Subject: Re: AMBER: PBradii


Hi Steve,
the data we showed in that Geney et al paper was for igb=1 and mbondi
radii, which is much worse at ion pairs
than igb=5 and mbondi2. The igb=5/mbondi2 is better, and in that system
the pmf was closer to
that from TIP3P (interestingly the reviewers asked us to remove that
We have some recent data using igb=5 (GB-OBC)/mbondi2 for a few other
salt bridging peptides, and
find for one that the PMF is almost the same as TIP3P, and for the other
the PMF is about 3 kcal/mol
too stable using GB. We have not tried modifying radii for use with
igb=5, so it's hard to say whether you
should reduce them or not especially since we get mixed results with the
mbondi2 set.

Having said that, implicit solvent might be the wrong way to go for a
large system. The computational
effort per time step can be much larger since PME is quite efficient in
a periodic system. You
will likely find that explicit solven can be much cheaper per time step,
and you only gain by
using implicit solvent if you are helped by the low viscosity.

On 9/11/07, Steve Seibold <> wrote:


I have been reading Geney et al from Carlos Simmerling's group about
born radii in AMBER and the "over stabilization" of the salt bridges
when using implicit solvent. I am doing some simulations where I am
"pulling" a ligand from its interior binding site in a protein (crystal
structure) a few angstroms to another site thought to be its entrance
location. I want to use implicit solvent because this is such a large
(gigantic) protein complex. I have applied igb = 5 and mbondi2. However,
I am worried after reading this paper that I should change the born
radii of my hydrogens bound to N-plus atoms from 1.3 to 1.1. The radii
suggested by the paper. Is there a way to do this in AMBER?


Thanks, Steve


Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
Center for Structural Biology       Fax:   (631) 632-1555 
CMM Bldg, Room G80
Stony Brook University              E-mail:
Stony Brook, NY 11794-5115          Web:
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Received on Wed Sep 12 2007 - 06:07:48 PDT
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