Thank you for your suggestion. I didn't think about it before.
Now I tried to use the pdb files of the molecule before and after
minimization with Gaussian03. Acdoctor doesn't detect errors directly in
them, but after antechamber it does again.
Interestingly, if I use antechamber -j 5, it doesn't detect the double
bond between C and N and acdoctor gives:
Error: weird atomic valence (2) for atom (ID: 5, Name: N),
possible have open valence
And if I use antechamber -j 4:
Error: weird atomic valence (5) for atom (ID: 11, Name: C3),
please check atomic connectivity
These atoms are the ones involved in the double bond of the
heterocycle.
Maybe there is some (simple?) way of solving it using bondtype, but I
didn't succeed at this.
Maybe the best approach is really to fix the central ring as having
conjugated double bonds instead of being explicitly aromatic, but I didn't
find out how to do this yet.
Here is the raw pdb:
ATOM 1 H H 1 0.600 -2.488 -1.742 1.00 0.00
H
ATOM 2 C C 1 0.167 -2.400 -0.729 1.00 0.00
C
ATOM 3 H H 1 0.792 -2.991 -0.034 1.00 0.00
H
ATOM 4 H H 1 -0.836 -2.869 -0.755 1.00 0.00
H
ATOM 5 N N 1 2.443 -0.891 -0.544 1.00 0.00
N
ATOM 6 C C 1 -2.306 1.646 0.753 1.00 0.00
C
ATOM 7 N N 1 0.077 1.742 0.503 1.00 0.00
N
ATOM 8 O O 1 2.510 3.087 0.616 1.00 0.00
O
ATOM 9 C C 1 -3.482 0.949 0.684 1.00 0.00
C
ATOM 10 O O 1 4.715 -0.660 -0.731 1.00 0.00
O
ATOM 11 C C 1 1.298 -0.267 -0.230 1.00 0.00
C
ATOM 12 C C 1 -3.491 -0.403 0.286 1.00 0.00
C
ATOM 13 N N 1 3.628 1.226 -0.060 1.00 0.00
N
ATOM 14 N N 1 0.113 -0.981 -0.304 1.00 0.00
N
ATOM 15 C C 1 1.195 1.132 0.194 1.00 0.00
C
ATOM 16 C C 1 -2.328 -1.055 -0.041 1.00 0.00
C
ATOM 17 C C 1 3.630 -0.137 -0.457 1.00 0.00
C
ATOM 18 C C 1 -1.088 0.997 0.420 1.00 0.00
C
ATOM 19 C C 1 2.459 1.909 0.276 1.00 0.00
C
ATOM 20 C C 1 -1.099 -0.361 0.020 1.00 0.00
C
ATOM 21 H H 1 -2.356 -2.110 -0.349 1.00 0.00
H
ATOM 22 H H 1 -4.448 -0.939 0.239 1.00 0.00
H
ATOM 23 H H 1 -2.288 2.699 1.062 1.00 0.00
H
ATOM 24 H H 1 -4.430 1.437 0.938 1.00 0.00
H
ATOM 25 H H 1 4.523 1.728 -0.014 1.00 0.00
H
END
Thank you in advance,
Leandro Bortot
2013/2/8 David A Case <case.biomaps.rutgers.edu>
> On Fri, Feb 08, 2013, Leandro Bortot wrote:
>
> > Error: weird atomic valence (5) for atom (ID: 11, Name: C3), please check
> > atomic connectivity
>
> Have you tried using a pdb format file as input to antechamber, which
> doesn't
> have any input bond orders (or bonds at all)?
>
> If that doesn't help, can you post the pdb file so that we can try to debug
> what is going on?
>
> ...thx...dac
>
>
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Received on Fri Feb 08 2013 - 10:30:04 PST
