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
--
--------------------------------------------------------------------------
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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.<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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Received on Wed Jun 21 2006 - 06:07:11 PDT
