From: Toshifumi Yui <>
Date: Wed, 21 Dec 2011 10:31:30 +0900

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.

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.
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 ?
In this case, I will continue test causations to check what will happen.

Toshi Yui

-----Original Message-----
From: Jason Swails
Sent: Wednesday, December 21, 2011 6:21 AM
To: AMBER Mailing List
Subject: Re: [AMBER] MM_PBSA

You should typically use the radius set that the GB model was parametrized
with. Therefore, I would make sure to generate topology files with the
appropriate radius set if you were trying to use your results for some kind
of publication.

It's OK for a demonstration and probably more important for dynamics to use
the correct radii, but it's generally good practice to use parameters that
were designed together.

I also recommend you use tleap when generating your topologies, as I've had
problems with sleap in the past setting the GB radii correctly.


On Tue, Dec 20, 2011 at 8:41 AM, Toshifumi Yui

> As working with tutorial 3 of MM_PBSA, I found the following message in
> the
> igb=2 should be used with mbondi2 pbradii set.....
> So I have carried out another trial calculations using a set of trmtop
> files
> created with "set default PBradii mbondi2" command, which gave different
> energy values for both GB and PB methods.
> Also I've got the same message again in the FINAL_RESULTS_MMPBSA.dat file
> produced by the trial calculations.
> I wonder that I don't have to worry about this warning any way, and is
> this
> Ok to use the trmtop files based on the normal PBradii setting according
> to
> the tutorial, even using igb = 2 option ?
> I am very confusing.
> Thank you
> Regards.
> Toshi Yui
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list 
AMBER mailing list
Received on Tue Dec 20 2011 - 18:00:02 PST
Custom Search