AMBER Archive (2006)

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

From: Christophe Guilbert (cguilbert_at_picasso.ucsf.edu)
Date: Mon Jun 19 2006 - 20:00:29 CDT

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.

Chris

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
quit
---------------------------------------------------

tleap -f leap.inp 

-- 
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Christophe Guilbert, Ph.D.
Mission Bay Genentech Hall
UCSF, Department of Pharmaceutical Chemistry
600 16th Street, Suite # S-126-D
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Office      : 415-476-0707
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Email: cguilbert_at_picasso.ucsf.edu
http://mondale.ucsf.edu
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@<TRIPOS>MOLECULE
ZINC00157587
   18 19 0 0 0
SMALL
USER_CHARGES
1H-benzoimidazol-2-amine
@<TRIPOS>ATOM
      1 C1 2.4380 2.5514 2.5630 C.ar 1 <0> -0.1500
      2 C2 1.5891 2.8096 3.6607 C.ar 1 <0> -0.1500
      3 C3 2.0882 2.9626 4.9624 C.ar 1 <0> -0.1090
      4 C4 3.4663 2.8433 5.0949 C.ar 1 <0> 0.3090
      5 C5 4.3062 2.5879 4.0089 C.ar 1 <0> 0.3090
      6 C6 3.8275 2.4338 2.7136 C.ar 1 <0> -0.1090
      7 N1 5.5867 2.5379 4.5203 N.pl3 1 <0> -0.8667
      8 C7 5.5588 2.7470 5.8381 C.cat 1 <0> 1.0700
      9 N2 6.6306 2.7671 6.6623 N.pl3 1 <0> -0.8367
     10 H1 6.4257 2.3671 3.9744 H 1 <0> 0.4500
     11 H2 6.5187 2.9344 7.6577 H 1 <0> 0.4500
     12 H3 7.5677 2.6154 6.3013 H 1 <0> 0.4500
     13 H4 2.0009 2.4408 1.5726 H 1 <0> 0.1500
     14 H5 0.5173 2.8919 3.4909 H 1 <0> 0.1500
     15 H6 1.4486 3.1608 5.8127 H 1 <0> 0.1500
     16 H7 4.4896 2.2361 1.8806 H 1 <0> 0.1500
     17 N3 4.2877 2.9328 6.1999 N.pl3 1 <0> -0.8667
     18 H8 3.9715 3.1134 7.1477 H 1 <0> 0.4500
@<TRIPOS>BOND
     1 1 6 ar
     2 1 2 ar
     3 1 13 1
     4 2 3 ar
     5 2 14 1
     6 3 4 ar
     7 3 15 1
     8 4 5 ar
     9 4 17 1
    10 5 6 ar
    11 5 7 1
    12 6 16 1
    13 7 8 1
    14 7 10 1
    15 8 9 1
    16 8 17 2
    17 9 11 1
    18 9 12 1
    19 17 18 1

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