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PostPosted: Sun Mar 08, 2015 7:55 pm 
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I've noticed a difference between Gasteiger charges added to ligand in adt and those computed with Openbabel or antechamber. Googling led me to unclosed bug: http://mgldev.scripps.edu/bugs/show_bug.cgi?id=214
Seaching through this forum I found that Pybabel Gasteiger charges were used for Autodock4 calibration: viewtopic.php?f=9&t=1398#p3928

Looking through the code of gasteiger.py (MGLToolsPckgs/PyBabel/gasteiger.py), I found 2 bugs:

1. Babel type HC hydrogens were assigned incorrect hybridD parameter (a+b+c instead of 20.02 as in paper of J. Gasteiger and M. Marsili, Tetrahedron 36, 3219 (1980))
Around line 362:
Quote:
hybridD = a2._gast_par[3]
if a2._xx > a._xx: hybridD = a._gast_par[3]
if a.babel_type == 'H': hybridD = 20.02
if a2.babel_type == 'H': hybridD = 20.02
a.gast_charge = a.gast_charge + \
(a2._xx - a._xx)/hybridD*z1


should be replaced by:
Quote:
hybridD = a2._gast_par[3]
if a2.babel_type[0] == 'H': hybridD = 20.02 #edited by KM
if a2._xx > a._xx: hybridD = a._gast_par[3]
if a.babel_type[0] == 'H': hybridD = 20.02 #edited by KM
a.gast_charge = a.gast_charge + \
(a2._xx - a._xx)/hybridD*z1


2. The initial electronegativity should be computed considering the formal charges
Around line 342:
Quote:
if a.babel_type == "N3+": a.gast_charge = 1.0
elif a.babel_atomic_number==8: # oxygens
if a.babel_type=="O-": a.gast_charge = -0.5
a._xx = a._gast_par[0]

should be replaced by:
Quote:
if a.babel_type == "N3+": a.gast_charge = 1.0
elif a.babel_atomic_number==8: # oxygens
if a.babel_type=="O-": a.gast_charge = -0.5
a._xx = a._gast_par[0] + a._gast_par[1] * a.gast_charge + \
a._gast_par[2] * a.gast_charge * a.gast_charge #edited by KM


Nevertheless the charges for my ligands are still differ. The point is that in PyBabel only sigma Gasteiger charges are calculated. My ligands contain pi-conjugated systems including nitrogen. In antechamber I see that these nitrogens are assined type na that has different Gasteiger parameters than Npl type which is assigned to these nitrogens in adt.


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