AMBER Archive (2007)

Subject: Re: AMBER: MM_PBSA No radius found for Br!!

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Tue Aug 14 2007 - 08:49:06 CDT


thank you for your email, so i should add

 "Br" => 1.500 + 1.850, ?

Is that right ?

thank you for any reply

Best Regards,
Urszula Uciechowska

MSc.PhD Student
Medicinal Chemistry Group
University of Halle-Wittenberg

----- Original Message -----
From: Antonio Morreale <amorreale_at_cbm.uam.es>
Date: Monday, August 13, 2007 1:40 pm
Subject: Re: AMBER: MM_PBSA No radius found for Br!!
To: Urszula Uciechowska <amber_at_scripps.edu>

> Hi,
>
> > How to set radius of Br in MMPBSA calculation. there is a Br atom
> in my ligand.
> > Could someone tell me where in which file i should add the line
> "Br 1.50" ?
> > my MMPBSA calculation gave me following info(i am using Amber9)
>
> Please, look for the mm_pbsa_calceneent.pm file. The search within it
> the subroutine generate_pqr(), here you can introduce the radius for
> Br. Those are Bondi radii, and for Br is 1.85 A
>
> Hope this helps,
> Antonio
>
> --
> Antonio Morreale
> Unidad de Bioinformática
> Centro de Biología Molecular "Severo Ochoa"
> Universidad Autónoma de Madrid
> Cantoblanco, 28049 Madrid (Spain)
> Phone: (34) 91-497-2377
> Fax: (34) 91-497-4799
> e-mail: amorreale_at_cbm.uam.es
> web: http://ub.cbm.uam.es/
>
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