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

From: Scott Brozell <sbrozell.scripps.edu>
Date: Sun, 19 Aug 2007 10:40:20 -0700

Hi,

On Tue, 14 Aug 2007, Urszula Uciechowska wrote:

> 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, ? ??

Do you want a Br radius of 1.50 or a Bondii Br radius of 1.85 ?

mm_pbsa_calceneent looks clear to me:

# Bondi radii + 1.4A and probe radius of 0.0A yields SAS
# Bondi radii + 0.0A and probe radius of 1.4A yields molecular surface
# Bondi radii + 0.0A and probe radius of 0.0A yields vdW surface
my %exp_rad = (
"N" => 1.550 + 1.400,
"H" => 1.200 + 1.400,
"C" => 1.700 + 1.400,
"O" => 1.500 + 1.400,

Scott

> > ----- 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>
> >
> > > > 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
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Received on Wed Aug 22 2007 - 06:07:09 PDT
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