Re: [AMBER] Atom type parameterization and prmtop file

From: David A Case <>
Date: Sun, 25 Jan 2015 21:34:47 -0500

On Mon, Jan 26, 2015, asdda asa wrote:
> 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.

It is certainly possible that antechamber is making a mistake with your
particular ligand. Please double-check your reasoning, however, since
alternate Lewis structures are often possible. If you wish, post the details
of your molecule -- we can't say more without more information.

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

I would certainly recommend doing a minimization using GAFF, and comparing
that to a minimization with a quantum code, e.g. using DFT or MP2. A lot
depends on what sort of simulation you are planning to do.

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

(a) read section 13.2 of the manual (the chapter on ParmEd);
(b) type "" to start parmed, then type "help"


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Received on Sun Jan 25 2015 - 19:00:02 PST
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