AMBER Archive (2008)

Subject: Re: AMBER: note on the molsurf and "Assertion `sarg1 >= 0.0' failed" error

From: Kateryna Miroshnychenko (kateryna_mirosh_at_ire.kharkov.ua)
Date: Tue Jun 03 2008 - 02:05:51 CDT

Well, this pqr file was generated by mmpbsa skript, by its subroutine
generate_pqr. Please see it below. I didn't change it. The last coloumn is
not diameters but Bondi radii + 1.4A. The probe radii used with this file is
0.0A. See the first comment of the generate_pqr. So I think that pqr file is
OK. May be I miss something, so please correct me...

regards, Katya

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);
}
> Your pqr file is flawed: it looks like you have *diameters* and not radii
> in the final column of the pqr file. I'm not sure how you prepared this
> file (maybe there is a bug somewhere else?) but you need to divide the
> final column numbers by a factor of two.
>
> ...good luck...dac
>
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