AMBER Archive (2007)

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

From: Urszula Uciechowska (urszula.uciechowska_at_pharmazie.uni-halle.de)
Date: Tue Aug 14 2007 - 10:53:32 CDT

Can someone tell me if its right?
I added to the file mm_pbsa_calceneet.pm

 "Br" => 1.500 + 1.400, ? it is right or should be

   "Br" => 1.500 + 1.850, ? ??

thank you in advance

Best Regards,
Urszula Uciechowska

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

----- Original Message -----
From: Urszula Uciechowska <urszula.uciechowska_at_pharmazie.uni-halle.de>
Date: Tuesday, August 14, 2007 3:51 pm
Subject: Re: AMBER: MM_PBSA No radius found for Br!!
To: amber_at_scripps.edu

> 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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