AMBER: RE: Antechamber poorly define atom angles of a five ring system whichcauses NH2 and C not to be planar as expected

From: Junmei Wang <>
Date: Mon, 19 Jun 2006 22:08:56 -0500

Hi, Chris,
If you use a little bit large drms (drms > 0.015), you could get planar

In order to use as fewer atom types as possible, we only introduced sp3
C and Sp2 C for 3 and 4-memberred rings. Maybe we need to introduce
special atom types for five-memberred rings in the next version of gaff.

For the current version of gaff, one may create a special atom type, say
cx, for sp2 carbon in a five-memberred ring for those "trouble"
molecules. Then one modify $ACHOME/dat/ATCOR.DAT file to make cx be
corresponding to c2. Most parameters involved by cx are borrowed from
those of c2 when parmchk is used to generate unknown parameters. Finally
one need to modify a special bond angle or torsional angle parameter to
make the improved version of gaff work.

All the best


Hi again.

I was working on a small molecule (see attachment ), I calculated the
topology/parameter using Antechamber1.25 and tleap(Amber8). After
minimization, N1, N3, C7 and N2 was not planar as expected, even
so those atoms was defined as planar by Antechamber. The improper angles

and dihedral was correctly defined by Antechamber.
The culprit here was the poorly atoms angle parameter (C4 N3 C7), (N1 C7

N3), (C4 N3 H8), (N1 C7 N2) (and others) of the five atoms ring system
C3 N1 C7 N3 C4.
It looks like the 5 atoms ring was rather defined as a 6 atoms ring
system, their angle values were closed to 120deg where it should have
been closed to 109deg. if you fix the angle parameter with some
realistic values , it is planar again.

Any fix, anyone ??? ;-))
Thanks a lot.


Here was my script:

antechamber -nc 1 -rn lig -i tobeconvert.mol2 -fi mol2 -o lig_bcc.mol2
-fo mol2 -c bcc -j 4 -at gaff
parmchk -i lig_bcc.mol2 -f mol2 -o lig_bcc.frcmod

here is the 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.
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UCSF, Department of Pharmaceutical Chemistry
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Received on Wed Jun 21 2006 - 06:07:12 PDT
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