Dear AMBER users,
I'm having problems using antechamber to parametrize a molecule and I
would be very thankful if someone could help me.
The molecule is composed of three rings. Actually, it is the oxidized
Flavin group [1]. I did four minimization steps:
(1) Molecular Mechanics, using the Quasi-Newton Algorithm
(2) Molecular Mechanics, using the Steepest Descent Algorithm
(3) Semi-Empirical using RM1
(4) Ab initio at HF/6-31G* theory level.
Steps 1 and 2 were performed with Gabedit; 3 with MOPAC2012; and 4
with Gaussian03.
acdoctor doesn't complain about the mol2 file generated after the
minimizations. However, after I use antechamber on it, I get the following
error with acdoctor:
-- check weird bonds --
Error: weird atomic valence (5) for atom (ID: 11, Name: C3), please check
atomic connectivity
This always happens after antechamber with -j 4 or -j 5. I have tried
to use different protocols with the mol2 but this always happens. If I use
parmchk on the mol2 for which acdoctor doesn't complain, all generated
parameters are marked as "attention: needs revision".
This problematic atom is the C of the central ring that makes a double
bound with the N of the other ring. I believe that the problem is that this
C is, at the same time, doing a double bond with N, 2 singles with Cs of
the main ring and is also involved in the aromatic bond. Thus, the program
considers that it has valence 5.
Do you have any suggestions? Is there any way to tell antechamber that
the aromatic ring shouldn't be accounted as a full bond, or even to fix the
conjugated double bonds instead of making the ring aromatic without losing
the improper dihedrals parameters for making the ring planar?
Thank you in advance,
Leandro Bortot
[1]
http://upload.wikimedia.org/wikipedia/commons/0/01/Isoalloxazin.svg
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Received on Fri Feb 08 2013 - 08:30:02 PST
