[AMBER] Atom type parameterization and prmtop file

From: asdda asa <nadaafiva.gmail.com>
Date: Mon, 26 Jan 2015 08:57:41 +0800

Dear all,

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.

In the original paper, it was also stated that most of the failures of atom
type definition happen to conjugated/aromatic rings attached to large
aliphatic rings [10+ 4*n *(*n=* 0, 1, 2) membered rings].

So, with these failure in the ligand parameterization, could I proceed to
the molecular dynamics simulation?

My second question, how to use a tool like ParmEd or cpptraj to inspect the
prmtop file.

I would be happy to have any comment.


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Received on Sun Jan 25 2015 - 17:00:02 PST
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