AMBER Archive (2007)

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

From: Antonio Morreale (amorreale_at_cbm.uam.es)
Date: Mon Aug 13 2007 - 06:39:52 CDT

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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