AMBER Archive (2006)

Subject: AMBER: halogen bondi radii in mm_pbsa_calceneent.pm

From: Giulio Rastelli (rastelli.giulio_at_unimo.it)
Date: Fri Oct 27 2006 - 03:46:30 CDT

Hi,
in order to have MM-PBSA working with ligands having halogen atoms,
it is necessary to include halogen radii in mm_pbsa_calceneent.pm
(assuming one is using MOLSURF and not LCPO).
I think there is a format problem if you insert Cl and Br radii in
this file:
                  "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,
                  "F" => 1.470 + 1.400,
                  "Cl" => 1.750 + 1.400,
                  "Br" => 1.850 + 1.400,
                  "I" => 1.980 + 1.400,
                 );

While fluorine is recognized and given the correct radii in pqr file,
bromine is not. If I set "B" istead of "Br", then it works correctly.
In the .pm file there is a format stating:
       my( $card, $atnum, $atm1, $atm2, $alt, $resname, $resno,
$x, $y, $z) =
          unpack("a6 a5 x a a3 a a3 x2 a4 x4
a8 a8 a8", $line);

$atm1 is a single-character, which might explain why Cl and Br
are not recognized.
How would you advise to solve this problem?
Thanks a lot in advance for your help.
Best
Giulio 

-- 

Prof. Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Facolta' di Bioscienze e Biotecnologie
Universita' di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
-------------------------------------
tel 0039-059-2055145
fax 0039-059-2055131
www.scifar.unimore.it/on-line/Home/Gruppidiricerca/Prof.GiulioRastelli.html
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