AMBER Archive (2004)

Subject: AMBER: Bondi radii for BR and F in mm_pbsa calculation

From: S. Frank Yan (SYan_at_gnf.org)
Date: Tue Jul 20 2004 - 18:01:03 CDT

Hi,

We noticed an error message in the mm_pbsa calculations:

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

It was pinpointed to be in the mm_pbsa_calceneent.pm, in which the Bondi
radii for different types of atoms are generated in the molsurf
calculation:

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

  # 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,
                );
....

However, the parameters for BR and F are not there. I was wondering if
anyone has parameters for these elements which are compatible in this
type of calculation.

Thanks a lot,
Frank

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