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

From: Carlos Simmerling <>
Date: Thu, 06 Jul 2006 21:51:58 -0400

you should read the Jorgensen article that you listed.
the HO does not have a radius but the O that it is attached
to does, and it should not "collapse" on another atom unless there
is a very bad initial geometry, incorrect bond lengths or
maybe wrong atom type assignments.

this ahs been discussed many times and you should find what
you need in the archives or the Jorgensen article.

Christophe Guilbert wrote:

> 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,
> JACS,110,(1988),1657
> hw 0.0000 0.0000 OPLS Jorgensen,
> JACS,110,(1988),1657
> 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
> quit
> ---------------------------------------------------------------------
> tleap -f leap.inp
> Thanks
> Chris
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Received on Sun Jul 09 2006 - 06:07:17 PDT
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