AMBER Archive (2006)

Subject: Re: AMBER: RDII and epsilon of ho and hw wrong in gaff.dat ??!!!

From: Christophe Guilbert (
Date: Thu Jun 29 2006 - 20:06:29 CDT

Thanks Bill

I am not a chemist so I apology in advance if I mistaken , but If that's
true , all the hydroxyl hydrogen has zero radius. This is bad because
for instance (in my case) , the hydroxyl hydrogen has a charge of
+0.37370 and 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 radius are set to zero, is TIP3 water
the only reason ???

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)

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

Bill Ross wrote:

>In TIP3 water, H's have no radius and O's have 'fat' radius to
>enclose them. Perhaps this is the intended use for ho and likely
>for hw in gaff.
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Christophe Guilbert, Ph.D.
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