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.
HTH,
Jason
On Tue, Dec 20, 2011 at 8:41 AM, Toshifumi Yui
<tyui.cc.miyazaki-u.ac.jp>wrote:
> As working with tutorial 3 of MM_PBSA, I found the following message in
> the
> FINAL_RESULTS_MMPBSA.dat file.
>
> WARNINGS:
> 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
>
>
>
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> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Dec 20 2011 - 18:00:02 PST
