From: FyD <>
Date: Thu, 11 Dec 2008 12:42:20 +0100

Hi Silas,

> 2) I edit the gaussian options to: #HF/6-31g* scf=tight test pop=mk
> iop(6/33=2) iop(6/42=6) opt
> To my understanding: 6/42=6 specifies the density points in each
> layer, 6/33=2 (which is NOT documented in gaussian 03) prints out
> potential points and potentials. On

I look at

> is is also recommended to use iop(6/41=10) on top, which would add
> 10 concentric layers of points for each atom. Is this option
> recommended or is it a carryover?

If you are interested in deriving RESP charges as in regular AMBER
force fields DO NOT USE IOp(6/33=2,6/41=10,6/42=17). This set of
keywords presents indeed some advantages in some cases [the tutorial
should explain why these keywords are used instead of IOp(6/33=2):
this is really confusing for new users] but should NOT be used if your
goal is to follow what has been done. The reference is IOp(6/33=2) &
not IOp(6/33=2,6/41=10,6/42=17) !

See for instance a simple Gaussian input to compute a MEP (Connolly
surface) as defined in AMBER force field . (GFInput GFPrint are even not

SCF=Tight is not useful for single point/MEP computation (SCF=Tight is
only required in the geometry optimization step).

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).

Finally, I would suggest using "Opt=Tight" (in the geom. optimisation
step) instead of "Opt" as in some cases, some differences are

All that is described .

> 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
> According to /usr/local/amber9/examples/resp_charge_fit/water/* I should get:
> O1 -.568182
> H1 0.284091
> H2 0.284091
> Looking at the gaussian optimised geometry of the water molecule I
> find small deviatons in the angle H1-O1-H2 compared to the standart
> water angle. What is happening here? Can I trust the RESP charges
> for my own ligands?

See below

> Where can I find
> more complete examples, other than the ones in
> /usr/local/amber9/examples/resp_charge_fit/* as they only come with
> input for resp but no files that have been used before that.

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)

The computations have been done in less than 10 minutes using R.E.D.
They are available in.tgz files .

WATER-1/RESP-charges HF/6-31G*//HF/6-31G*
WATER-1/ESP-charges HF/6-31G*//HF/6-31G*
WATER-1/ESP-charges-Old HF/STO-3G//HF/6-31G*
WATER-2/ESP-charges-Old HF/STO-3G//HF/STO-3G

See [WATER-2/ESP-charges-Old]$ more Mol_m1-o1.mol2
   1 O1 0.000000 0.127160 0.000000 O 1 H2O -0.5623
   2 H2 0.758082 -0.508640 0.000000 H 1 H2O 0.2811
   3 H3 -0.758082 -0.508642 0.000000 H 1 H2O 0.2811

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 !

If you decide to compute charge values with those theory levels, you
will get such warning using R.E.D.:

               "ESP-A2" & "ESP-C2" charge models are outdated
      Nowdays, they should _not_ be used in atomic charge derivation
These models are only available in R.E.D. for compatibility with the past

> I apologize if the mailing list is not the right place to post.
> However, I am grateful for any pointers!

Reproducing, charge values is always difficult.

I would like to suggest you to use the R.E.D. program to do such work. Indeed, once you
got how R.E.D. works (need some time to get into it), you will
generate _reproducible_ data.
The R.E.DD.B. database is
associated to the R.E.D. program, & you can find tutorial .

I hope this helps.

regards, Francois

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Received on Fri Dec 12 2008 - 01:16:01 PST
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