My sincerely thanks, prof.
It is very helpful.
Thank you.
nadaafiva
On Wed, Jan 28, 2015 at 12:19 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Tue, Jan 27, 2015, asdda asa wrote:
>
> > Here I attach the molecule.
>
> > I am confusing with atom types in my ligand. In the original journal
> > of Gaff (J Comput Chem 25: 1157, 2004), both cc—cc and cd—cd
> > are assigned as conjugated single bonds, and cc—cd is conjugated
> > double bond. However in my ligand which was aromatic with 18 pi
> > electron, cc—cc was assigned as conjugated double bonds, and
> > cc—cd is conjugated single bond.
>
> I don't see the exact problem you are referring to, but I agree that
> antechamber is having trouble with the 4-methylpyridinium parts. This is a
> pretty evil molecule for automatic bond perception: the underlying
> four-fold
> symmetry is broken both the by two hydrogens in the middle of the ring, and
> (in a different way) by the fact that one of the meso substitutents is
> different from the other three.
>
> It looks like you need to assign bond types by hand here. You might try
> the
> parent molecule TMPyP, and modify one of the meso substitutents by hand.
> But
> you need to make sure that the bonds at the meso carbons (to the
> substitutents
> are single bonds.)
>
> ...good luck....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 27 2015 - 20:00:02 PST
