AMBER Archive (2009)
Subject: Re: [AMBER] Targeted MD and QM/MM
From: Gabriel Urquiza (urquizagabes_at_gmail.com)
Date: Tue Jun 02 2009 - 17:08:11 CDT
Thanks a lot Dr. Seabra!
I was trying to make a QM/MM with an enzym,e treating only its active site
as a quantum part. So I guess I'll be needing those topologies, anyway.
Well, thanks again for the tip, I hope I'll be able to untie that know now.
Post Graduation student
Universidade Federal da Paraíba - Brazil
2009/6/2 Gustavo Seabra <gustavo.seabra_at_gmail.com>
> 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 <urquizagabes_at_gmail.com>
> > 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
> > topology of our ligands and I'm not being exactly successful. The problem
> > 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
> > on the active site of the enzyme. I'm sending along the LEaP log of my
> > use.
> > Any help regarding this issue would be kindly welcome. I've been
> > 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 Paraíba - Brazil
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