Re: [AMBER] Atom type parameterization and prmtop file

From: David A Case <>
Date: Tue, 27 Jan 2015 11:19:33 -0500

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

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Received on Tue Jan 27 2015 - 08:30:03 PST
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