AMBER Archive (2008)

Subject: Re: AMBER: PB Radii

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Mon Nov 17 2008 - 05:30:41 CST

I would suggest finding articles in the literature that have
successfully done what you want and then see which methods they used.
This email list is more for technical questions and troubleshooting
amber, and not so much for recommendations on solving scientific
problems. for that you're better off trusting peer-reviewed
literature, in my opinion. while you may get a quick answer here,
there's really no way to know if the person posting has even done the
kind of calculation you want, or if the results have been properly
validated .

On Mon, Nov 17, 2008 at 6:24 AM, Swarup Gupta <swarupgupta_at_yahoo.com> wrote:
>
> Thank a lot for your response.
>
> Now I wish to know if I use igb=2 or igb=5 keeping the
> default dielectric radii set then the result would be worng or not reliable
> at all? I am trying to calculate binding free energy from MMGBSA calculation
> by postprocessing a trajectory which was originally run with explicit water.
>
> regards,
> S Gupta
>
>
>
> --- On Thu, 11/13/08, David A. Case <case_at_biomaps.rutgers.edu> wrote:
>
> From: David A. Case <case_at_biomaps.rutgers.edu>
> Subject: Re: AMBER: PB Radii
> To: amber_at_scripps.edu
> Date: Thursday, November 13, 2008, 6:01 AM
>
> On Wed, Nov 12, 2008, Swarup Gupta wrote:
>
>> I want to know if I use IGB=2 while keeping the default radii set then
>> whether the results would be wrong!! The manual says that "With this
> option,
>> you should use the LEaP command "set default PBradii
> mbondi2"......but my
>> confusion is that I am not working with PB; then what is the use of
> setting
>> a PBradii here while running GB?
>
> The term "PBradii" might better be named
> "continuum_electrostatics_radii" or
> "dielectric radii". They are used for both GB and PB calculations.
>
> ...dac
>
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