AMBER Archive (2008)

Subject: Re: AMBER: RE: Personal favor

From: fatima.chami_at_durham.ac.uk
Date: Mon Sep 01 2008 - 06:29:46 CDT

Hi Jason,

Another way to validate the force field parameters is to calculate the torsional
potential both in MM (umbrella sampling) and QM (potential energy surface scan)

best wishes
Fatima
Quoting Ross Walker <ross_at_rosswalker.co.uk>:

> 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
> mistakes.
>
>
>
> Good luck,
>
> Ross
>
>
>
> From: Jason Whitte [mailto:jason.whitte_at_gmail.com]
> Sent: Tuesday, August 26, 2008 2:55 PM
> To: ross_at_rosswalker.co.uk
> 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.
> Jason.
>
> 

-- 
Dr. F.Chami
Science Lab.
Department of Chemistry
Durham University
South Road Durham, DH 1 4 LE
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