AMBER Archive (2008)
Subject: RE: AMBER: RESP GAUSSIAN AMBER
From: FyD (fyd_at_q4md-forcefieldtools.org)
> Which reference is this specified in? I could never find a definitive
> document that specified exactly what options were used for Gaussian fits.
This means the tutorial @
There is obviously not a unique answer: It is why the different
> I think these options were found by the students that wrote this tutorial
> from the attached webpage. I have no idea what the history of this page is.
"these options were found _by_ the students" & "I have no idea".
Waouh ! Here, I prefer not answering...
> However, do you know if these options actually make a measurable difference?
Sure, there is a difference. Why do you think those options are used ?
> Sure they might give slightly different charges but then my experience with
> RESP is that it is only marginally reproducible at best anyway.
I am not sure I agree here (see below).
> It seems to
> me that, for example, upping the number of points per layer and the number
> of layers should simply result in the charges generated converging to a
> specific value as a function of the number of points used. If one gets
> different charges at the default settings then the default options are
> surely not large enough to obtain convergence in the results and will just
> lead to large error bars.
May be you should do some tests here, & explain this point in your
> I guess people should read the disclaimer at the top of all the tutorials:
> "These tutorials are meant to provide illustrative examples of how to use
> the AMBER software suite to carry out simulations that can be run on a
> simple workstation in a reasonable period of time. They do not necessarily
> provide the optimal choice of parameters or methods for the particular
> application area."
> The main purpose of the tutorials here is to take people through the steps
> involved in a way that lets them appreciate (and hopefully think!!!) about
> what is going on and avoid use of any black box approaches as much as
> possible. They don't attempt to discuss the complexities of MD simulations
> which make MD such a dynamic area of research.
Yes I agree, although convenient ;-)
A new user generally follows what is written (if there is no clear
I have a last comment about this tutorial; the worst one:
> Note that Antechamber (from the Antechamber source) uses:
> #HF/6-31G* SCF=tight Test Pop=MK iop(6/33=2) iop(6/42=6) opt
> Which includes the 6/42 option although with a value of 6 instead of 17.
Whatever the choices made - as I already said there is not a unique
> I'm not sure the SCF Tight comment is strictly true here.
SCF(Conver=8) in geometry optimization & SCF(Conver=6) in single point
This is indeed "strictly" true. Using SCF(Conver=6) one generates MEP
> Note Gaussian (at
> least in Gaussian 98) uses a very loose SCF convergence criteria for single
> point SCF calculations(something like 10^-4 if I remember, I don't have the
> manual to hand) which will certainly affect the results. I have not checked
> to what extent it effects the final RESP charges though. It certainly can't
> hurt to include SCF=Tight - it will just up the computational requirements.
For Water-3 atoms- & HF/6-31G* ? Sure.
But for complex force field topology database building using
>> I would also suggest you to use HF/6-31G* (or HF/6-31G**, Duan et al.
>> FF) in the geometry optimization step - if you do want to rigorously
>> follow what has been done (& not MP2/6-31G* or B3LYP/6-31G* as it is
>> described in this tutorial).
> Are you sure HF/6-31G* was used for geometry optimization in FF94 and
> subsequently FF99, 99SB etc? The original FF94 JACS paper is awful when it
> comes to describing exactly what was done but I find it hard to believe that
> HF/6-31G* was used for the optimization.
Yes, you are right this is difficult to not be lost. However, once
> Note Cornell et al. JACS 1993, 115,
> 9620 talks about MP3/6-31+G**//HF/6-31G* and MP2/6-31G*//HF/6-31G* and MM2
> but never mentions HF/6-31G*//HF/6-31G*. I don't have the FF03 paper to hand
> to check what Yong did (no internet connection at the moment).
Duan et al. use HF/6-31G** in the geometry optimization step before
> I am
> intrigued to know where you get the recommendation for HF/6-31G* geometry
> optimization from.
If one has as objective to follow a standard procedure or to develop a
>> > To get a feeling of whether this procedure is correct I had a look
>> > at /usr/local/amber9/examples/resp_charge_fit/water. I created a
>> > water molecule in molden and applied the same procedure (this time
>> > with and without option iop(6/41=10)). The obtained charge are
>> > basically identical:
>> > O1 -0.81327
>> > H1 0.40664
>> > H2 0.40664
> As I thought - upping the Gaussian precision does not impact the results.
Please, consider this water molecule case (-3 atoms-) quite basic as
>> I looked at your problem & computed RESP or ESP charges for water using
>> HF/6-31G*//HF/6-31G* (Cornell at al. FF, 1994-...)
>> or the olds:
>> HF/STO-3G//HF/6-31G* (Weiner at al. FF, 1984/1986)
>> HF/STO-3G//HF/STO-3G (Weiner at al. FF, 1984/1986)
>> This means the data available @
>> /usr/local/amber10/examples/resp_charge_fit/water/ have been generated
>> using HF/STO-3G//HF/STO-3G !
>> I guess they come from Amber... 4/3 ?. Do not use that as a reference !
> So if you use HF/6-31G*//HF-6-31G* can you reproduce the charges in the FF94
What does it mean "reproduce" ? with what error ? None of the charge
If you use R.E.D. the charge reproducibility achieved is +/-.0001
> All the force field parameter derivations, like bond lengths and angles were
> done using MP2/6-31G* (same for GAFF) so it makes sense that they would use
> the same for charges, although there is the discussion that HF/6-31G*
> overestimates the gas phase dipole moment which is beneficial for solution
> phase simulations but from what I can see the discussion was never very
> clear what geometry this referred to.
> Perhaps someone should volunteer to provide a tutorial on the AMBER website
> that goes through a step by step process for reproducing the FF94 / FF99 /
> FF99SB and FF03 parameters (charges, VDW and valence terms) for say Alanine.
> I think this would really help clear up lots and lots of confusion that
> exists in the "black art" of force field derivation.
Concerning charge derivation, I think you have more than that @
I hope this helps.