AMBER: FW: missing bondi radii of Br and F for surface area calculation

From: S. Frank Yan <SYan.gnf.org>
Date: Tue, 20 Jul 2004 10:30:13 -0700

Hi, I'm forwarding this message for a colleague regarding the Bondi
radii for BR and F. Thanks, Frank


Subject: missing bondi radii of Br and F for surface area calculation

Hi,

I got the following error when calculating the surface area.

Generate PQR
No radius found for BR
No radius found for F

This is the subroutine I found in mm_pbsa_calceneent.pm, it includes a
list of Bondi radii, but no Br and F. I am wondering if anyone has the
bondi radii values for these two elements.


sub generate_pqr(){
###################
 

  # This implementation uses bondi radii
 

  # Parameters: $pdb,$pqr,$r_mol
  my $pdb = shift;
  my $pqr = shift;
  my $r_mol = shift;
 

  # 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,
                 "P" => 1.800 + 1.400,
                 "S" => 1.800 + 1.400,
                 "FE" => 1.300 + 1.400,
                 "Na+" => 1.200 + 1.400,
                 "Cl-" => 1.700 + 1.400,
                 "MG" => 1.180 + 1.400,
                );
 

  print " Generate PQR\n";
  make_pqr_file($pdb,$pqr,\%exp_rad);
}
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Received on Tue Jul 20 2004 - 18:53:00 PDT
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