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
--
--------------------------------------------------------------------------
Christophe Guilbert, Ph.D.
Mission Bay Genentech Hall
UCSF, Department of Pharmaceutical Chemistry
600 16th Street, Suite # S-126-D
San Francisco, CA 94143-2180
for UPS/Fed Ex/DHL, change the zip code of 94107 for physical deliveries of package
Office : 415-476-0707
Office fax : 415-476-0688
Email: cguilbert.picasso.ucsf.edu
http://mondale.ucsf.edu
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Received on Sun Jul 09 2006 - 06:07:16 PDT
