RE: AMBER: QM/MM LJ parameters

From: Ross Walker <>
Date: Thu, 5 Jul 2007 17:58:49 -0700

Dear Evan,
I appreciate that the manual may not go into sufficient detail for the QM
calculations. We have a manuscript describing the QM/MM implementation in
detail that is currently pending with J Comp Chem. Hopefully it will be
published shortly and then you can refer to this for more details. In the
meantime the description below should help you:
The Lennard Jones parameters used for the QM-MM interactions are those
specified in the prmtop. They are not adjusted or scaled in any way. Thus if
you simply built your prmtop using e.g. FF99SB or GAFF then it will be the
parameters corresponding to the atom types in these force fields. So in
other words the 'default' MM parameters. If you wish to use a set of
'optimized' parameters then it is simple to do this at the prmtop creation
Start by making sure your QM region is defined as non standard residues and
give them unique atom types. You need to do this so you don't change the LJ
parameters for the MM atoms that share the same atom type. Then create a
frcmod file and specify in here the parameters you want to use. Note you
will also have to provide the mass for the atom type - just use the default
mass from the original type. You will also need to give bond, angle and
dihedral parameters in order to convince leap to write you a prmtop. Note
the actual parameters you choose here are irrelevant since they will simply
be ignored in the QM part of the calculation. EXCEPT: If you have qmshake
turned on the equilibrium distance of any bonds to hydrogen will be used for
shake. In addition any parameters that span the QM and MM regions will be
used in the calculation.
I hope this helps.
Good luck...

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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From: [] On Behalf Of
Evan Kelly
Sent: Thursday, July 05, 2007 16:32
Subject: AMBER: QM/MM LJ parameters

Hi Everyone,

I was hoping someone could explain where the parameters for the
Leonard-Jones forces (A and C in eq. 6.16 of the Amber 9 manual) are
obtained for the QM atoms in a QM/MM simulation. Are they the same as the MM
atoms or are they optimized for use in QM/MM methods?


Evan Kelly

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Received on Sun Jul 08 2007 - 06:07:33 PDT
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