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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Received on Wed Jul 21 2004 - 00:53:00 PDT
