AMBER Archive (2008)

Subject: Re: AMBER: RESP GAUSSIAN AMBER

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Dec 11 2008 - 05:42:20 CST

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
> http://ambermd.org/tutorials/advanced/tutorial/section1.htm

I look at http://ambermd.org/tutorials/advanced/tutorial1/section1.htm

> 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 @
http://q4md-forcefieldtools.org/Tutorial/3-Charges-Gaussian-A-QMRA/JOB2-gau_m1-1-1.com (GFInput GFPrint are even not
required)

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
observable...

All that is described @ http://q4md-forcefieldtools.org/Tutorial/.

> 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 @
http://q4md-forcefieldtools.org/FyD/WATER-1.tgz
http://q4md-forcefieldtools.org/FyD/WATER-2.tgz

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
[...]
@<TRIPOS>ATOM
   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.:

                               WARNING:
               "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
http://q4md-forcefieldtools.org/RED/ 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. http://q4md-forcefieldtools.org/RED/ database is
associated to the R.E.D. program, & you can find tutorial @
http://q4md-forcefieldtools.org/Tutorial/

I hope this helps.

regards, Francois

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu