Dear Amber users,
I find in mm_pbsa/mm_pbsa_calceneent.pm
# 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);
}
Who can give me the radius of F,Cl,Br,or the reference paper?
Thanks in advance!I appreciate.
Xiao He
hx.itcc.nju.edu.cn
2004-10-24
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Oct 24 2004 - 15:53:00 PDT
