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.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.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.cbm.uam.es
> web: http://ub.cbm.uam.es/
>
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Received on Wed Aug 15 2007 - 06:07:49 PDT
