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
