AMBER Archive (2004)

Subject: AMBER: continue for No radius for F atom in MM_PBSA

From: Xiao He (hx_at_itcc.nju.edu.cn)
Date: Sun Oct 24 2004 - 09:40:21 CDT

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_at_itcc.nju.edu.cn
　　　　　　　　　　2004-10-24

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu