AMBER Archive (2009)

Subject: Re: [AMBER] Targeted MD and QM/MM

From: Gustavo Seabra (
Date: Tue Jun 02 2009 - 09:43:35 CDT

Hi Gabriel,

You do need a working prmtop file for running QM/MM calculations in
Amber. If you don't plan on running any MM calculations with it, then
most parameters can be bogus, just so Amber can load the molecule, but
you still need them.

You don't mention how you prepared the parameters for your ligand, so
its hard to see where exactly is the problem, but looking at the
leap.log file I'd recommend the following:

1. Use antechamber to generate gaff parameters for your molecule.

2. It seems that you are using ff03 force field. Although it's a good
force field,
    it is not compatibel with GAFF. You should use ff99SB instead.

All the best,
Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
Q: Why do mountain climbers rope themselves together?
A: To prevent the sensible ones from going home.

On Fri, May 29, 2009 at 4:09 PM, Gabriel Urquiza <> wrote:
> Dear AMBER users,
> I'm pretty new in this AMBER business, and pretty interested in doing a
> Targeted MD of a new ligand in the active site of Farnesyl Pyrophosphate
> Synthase (1YHL). I'm following exactly the Efavirenz tutorial to build the
> topology of our ligands and I'm not being exactly successful. The problem is
> that the atom types for my ligand A0N can't be determined, and so I can't
> build my topology and coordinate files for the complex enzyme-ligand. I
> would also like to ask if that is strictly neccessary for performing QM/MM
> on the active site of the enzyme. I'm sending along the LEaP log of my last
> use.
> Any help regarding this issue would be kindly welcome. I've been struggling
> with this problem for ages now and it is really depressing to get error
> messages around twenty times a day. Please help.
> Gabriel Urquiza
> Post graduation student. Universidade Federal da Paraba - Brazil

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