AMBER: RE: Personal favor

From: Ross Walker <>
Date: Thu, 28 Aug 2008 09:39:59 -0700

Hi Jason,


This is really the $64,000 question. Stating how 'accurate' a set of force
field parameters are is very hard and a very subjective question. The best
you can typically do is carefully justify your choice of parameters in the
first place. Typically I would only blindly trust antechamber for things
such as ranking a set of ligands against each other. If you are looking at a
specific system in detail then you should probably parameterize it yourself
or carefully check what antechamber assigns for various dihedrals etc. I
just think that anything that relies on a lot of subtle dihedral
interactions is going to be tricky for antechamber to get correct.


A simple check you could do is just to look at the correlation between the
MM energies and a series of MP2 energies. So for example take a few hundred
snapshots of structures for trehalose from MD, extract them so that they are
gas phase and run single point calculations on them in AMBER to give you the
gas phase amber energy of each snapshot. Then for each of these structures
also do say a MP2/6-31++G** single point calculations. Then plot the
energies against each other (x=MM, y=MP2) and see if you get a reasonable
straight line with a gradient of 1.


You could also try comparing normal modes, between a QM calculation and a
run using nmode and the MM parameters. This will show you if there are any
dihedrals for example that are wildly wrong.


If someone else generated these files for you my first approach as well
would be to regenerate the RESP charges yourself and also manually check all
the atom type assignments etc to make sure that they didn't make any basic


Good luck,



From: Jason Whitte []
Sent: Tuesday, August 26, 2008 2:55 PM
Subject: Personal favor


Hello Ross,
This is regarding parameters of trehalose generated by a combination of
Gaussian and antechamber. I was given this coordinate set by a colleague who
has since left our group. I was wondering how accurate the parameter set is.
Could you please take a look at the file attached and comment on how I can
verify its accuracy? I have come under a lot of fire regarding the dynamics
of trehalose that I have obtained from simulations and I am in the process
of finding any potential mistakes in my research and I guess the first place
is to check the force field parameters.
Thank you very much for your time.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Sun Aug 31 2008 - 06:07:36 PDT
Custom Search