AMBER Archive (2008)

Subject: RE: AMBER: QM/MM simulation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Nov 22 2008 - 10:59:49 CST

Hi Syed,

> But do you think about SCF-DFTB support for Iron as mentioned in manual as
> implemented in amber10.

I assume you are referring to the trans3d parameter set on DFTB.org. I have
not actually tried this parameter set so don't know how it performs but
Gustavo may be able to comment more - he may have tried it.

As Dave said you will need some form of parameters for the QM region since
Leap requires this to build a prmtop. At the very least for QM atoms (away
from the QM/MM boundary) you need to have the mass and VDW terms defined
(since QM/MM interactions use the VDW parameters). You can leave out the
bonds for most of what will be the QM region so you do not need to provide
bond, angle and dihedral parameters (that will be ignored) or alternatively
you can just set these all to dummy values of your choosing (say force
constant = 0.0) in the frcmod file.

Within 3 bonds of the QM/MM boundary (if you are cutting bonds in forming
your QM region) then you need to include real parameters since these will be
needed. Bond, angle and dihedral terms that include at least one MM atom are
calculated classically so the parameters are needed here. Additionally if
you plan to use shake on the QM region then you need valid equilibrium bond
lengths for bonds to hydrogens specified.

The easiest solution if you have a classical system setup already is to just
use the prmtop from this. You probably want to run some NVT and NPT
equilibration classically before switching to QM/MM anyway to save you time.

Good luck,
Ross

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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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