AMBER: Why "ho" and "hw" VDW's radius are set to 0 in "gaff.dat" ?

From: Christophe Guilbert <>
Date: Thu, 06 Jul 2006 17:51:49 -0700

When minimizing one of my ligand which include one "ho" atom type, I
found that it collapsed (superimposed) with its nearest atom generating
a crazy electrostatic energy. this comes from the fact that I am using
the VDW radius value in "gaff.dat" for "ho" which has a VDW radius and
epsilon set to 0.0000.
 ho 0.0000 0.0000 OPLS Jorgensen,
 hw 0.0000 0.0000 OPLS Jorgensen,
What happened (see attatchment) when I minimize the ligand is that the
hydroxyl hydrogen "ho" which has a charge of +0.37370 collapse on a
neighboring C(type c3) which has a charge of -0.62100. Since there is no
VDW radius to the hydrogen, both atoms of opposite charge are very
attracted and collapse.

I can change the gaff.dat file and add a VDW radius to those guys, but I
would like to understand why those VDW radius are set to zero.
I assume that tleap read "gaff.dat" , does tleap correct "ho" and "hw"
VDW radius later at some point ?

Please would you find in the attachment the pdf file of the ligand if
anyone want to try it. monitor HO3 (atom 11) collapsing on C2(atom 3)
after minimization (structure liga_mini.pdb)

the following is the script I used to generate the topology and parameter.
antechamber -nc -5 -rn lig -i liga_regul.pdb -fi pdb -o lig_bcc.mol2 -fo
mol2 -c bcc -j 4 -at gaff -pf y
parmchk -i lig_bcc.mol2 -f mol2 -o lig_bcc.frcmod

--------leap.inp file --------------------------------------------
source leaprc.gaff
mods = LoadAmberParams lig_bcc.frcmod
lig = loadMol2 lig_bcc.mol2
saveAmberParm lig lig_bcc.prmtop lig_bcc.prmcrd
tleap -f leap.inp



Christophe Guilbert, Ph.D.
Mission Bay Genentech Hall
UCSF, Department of Pharmaceutical Chemistry
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Received on Sun Jul 09 2006 - 06:07:16 PDT
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