AMBER Archive (2008)

Subject: Re: AMBER: output effective Born radii

From: Holly Freedman (freedman_at_phys.ualberta.ca)
Date: Mon Mar 10 2008 - 21:24:32 CDT

Hi Prof. Case,
Thank you very much for your reply. For the program I am using, I was told that it should be OK to
use the AMBER effective Born radii as long as I also use the charges from AMBER.
Best regards,
Holly

> On Mon, Mar 10, 2008, Holly Freedman wrote:
>
> > I am attempting to use a CHARMM-based program that asks for effective
> > Born radii in one of the columns of the input pdb. I am not a CHARMM
> > user though and I don't have the CHARMM code installed, and so if
> > possible I would like to calculate these radii using AMBER. Is there
> > a way to get AMBER to output these Born radii?
>
> See the "rbornstat" variable, which does what you want. Except(!), it outputs
> the effective radii from the *Amber* gb models, which will be different than
> from CHARMM gb models. There may be important differences between these.
>
> ...dac
>
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--
Department of Physics, University of Alberta
Edmonton CANADA

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