AMBER Archive (2003)

Subject: Re: Re[2]: AMBER: derive corresponding torsional parameters

From: David Smith (David.Smith_at_cup.uni-muenchen.de)
Date: Fri Aug 08 2003 - 11:20:32 CDT

Dear sychen,

On Fri, 2003-08-08 at 17:43, sychen wrote:
> Dear David Smith:
>
> Thanks for your kind help.
> I understand what you have mentioned, but what confuses
> me is that my system contains 51 atoms, however I'd like
> to derive just one torsion energy from the PES calculation.
>
> Or it is reasonable to evaluate it from the total SCF energy
> owing to the contribution of the different torsion energy
> by systematically changing the specific torsion angle?

Basically, yes. It is reasonable to evaluate it from the variation in
the total SCF energy obtained by systematically changing the torsion
angle.

This statement comes with the following qualifiers:

Worst would be a rigid scan that just changes the dihedral and leaves
everything else rigid.

Better would be a relaxed scan which optimizes all other parameters for
each dihedral angle.

Best would be to use one or other of the above to identify approximately
which value of the dihedral the torsional transition state(s) lie(s).
Use this as a starting guess for an opt=ts type of calculation and
calculate the TS for rotation exactly. This is more like the "The
relative energies of three stationary points on the energy surfaces were
selected to derive the corresponding torsional parameters" approach that
you mentioned before.

With 51 atoms and HF theory, you can do this relatively easily on most
modern computers.

Alternatively, if you were to follow the "AMBER" force field development
strategy, you may want to consider a simpler, representative, fragment
in which to investigate the torsions and assume the transferability of
the parameters to larger systems. In this respect, you could use DFT
with a larger basis set (e.g. B3LYP/cc-pVTZ) to get a more accurate
number for the torsional barrier.

You should, of course, be careful to get the periodicity right.

Finally, others may have different (or better) approaches so you
shouldn't necessarily take everything I say to be correct.

Good luck.

David.

> Best Regards,
> sychen.
>
>
> On 08 Aug 2003 15:39:57 +0200
> David Smith <David.Smith_at_cup.uni-muenchen.de> wrote:
>
> > Dear sychen,
> >
> > If the scan worked you should get a section like:
> >
> > ***********************************************
> >
> > Scan completed.
> >
> > Summary of the potential surface scan:
> > N D3 SCF
> > ---- --------- -----------
> > 1 180.0000 -78.78894
> > 2 160.0000 -78.78749
> > 3 140.0000 -78.78459
> > 4 120.0000 -78.78313
> > 5 100.0000 -78.78459
> > 6 80.0000 -78.78749
> > 7 60.0000 -78.78894
> > 8 40.0000 -78.78749
> > 9 20.0000 -78.78459
> > 10 0.0000 -78.78313
> > 11 -20.0000 -78.78459
> > 12 -40.0000 -78.78749
> > 13 -60.0000 -78.78894
> > 14 -80.0000 -78.78749
> > 15 -100.0000 -78.78459
> > 16 -120.0000 -78.78313
> > 17 -140.0000 -78.78459
> > 18 -160.0000 -78.78749
> > 19 -180.0000 -78.78894
> > ---- --------- -----------
> > *********************************************
> >
> > almost at the very end of the output. The above output is from a simple
> > example for the ethane torsion that I just did using the following
> > input:
> >
> > **********************************************
> >
> > # rhf/3-21g scan nosym
> >
> > example scan, ethane
> >
> > 0 1
> > C
> > C 1 B1
> > H 1 B2 2 A1
> > H 1 B3 2 A2 3 D1
> > H 1 B4 2 A3 3 D2
> > H 2 B5 1 A4 3 D3
> > H 2 B6 1 A5 6 D4
> > H 2 B7 1 A6 6 D5
> >
> > B1 1.500250
> > B2 1.117137
> > B3 1.117137
> > B4 1.117137
> > B5 1.117137
> > B6 1.117137
> > B7 1.117137
> > A1 110.724835
> > A2 110.724835
> > A3 110.724835
> > A4 110.724835
> > A5 110.724835
> > A6 110.724835
> > D1 120.0
> > D2 -120.0
> > D3 180.0 s 18 -20.0
> > D4 -120.0
> > D5 120.0
> >
> > *******************************************
> >
> > There are a few things to note.
> >
> > This changes the value of the dihedral angle "D3" from 180 degrees by
> > -20 degrees over 18 steps.
> >
> > I prefer to use a z-matrix in a scan as I can better control what's
> > going on than with "redundant internal coordinates".
> >
> > It is usually a good idea to turn symmetry off (nosym) as often the
> > scanning coordinate will break the symmetry (as it does in this case).
> >
> > The above scan is a "rigid scan". This means that the structures are not
> > optimized at each step, the dihedral is simply changed and the energy
> > calculated.
> >
> > If you replaced "scan" with "opt=z-matrix" you would optimize all other
> > parameters (except D3) at each step. If the system is not too big then
> > this is probably the way to go.
> >
> > I guess you are already aware but the energy units are Hartrees and 1
> > Hartree is equivalent to 627.5 kcal/mol.
> >
> > I think that's about all. If you have any more questions, please don't
> > hesitate to ask.
> >
> > Good Luck.
> >
> > David.
> >
> > On Fri, 2003-08-08 at 12:25, yuann wrote:
> > > Dear All,
> > >
> > > Is there any reference or document to understand the
> > > followings,
> > > 'The relative energies of three stationary
> > > points on the energy surfaces were selected to derive
> > > the corresponding torsional parameters.',
> > > which is described in Junmei et al. 1999.
> > >
> > > It seems to be that the method is described in Appendix C,
> > > 'Parameter Development'. If so, how to derive the
> > > specific torsional energy from Gaussian98's output?
> > > because I could just get the whole energy of the
> > > molecule after the potential energy surface scans.
> > > I'm sorry if this is an easy question, because I'm
> > > not very familiar to Gaussian.
> > >
> > > Thank you for your help in advance.
> > >
> > > Best Regards,
> > > sychen.
> > >
> > >
> > > -----------------------------------------------------------------------
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> > --
> > ---------------------------------------
> > Dr. David Smith
> > Department of Chemistry
> > Ludwig Maximilians University
> > Butenandt-Str. 5-13, D-81377 Munich
> > Germany
> > Tel.: +49 (0)89 2180 77740
> > Fax.: +49 (0)89 2180 77738
> > e-mail: David.Smith_at_cup.uni-muenchen.de
> > ---------------------------------------
> >
> >
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>
>
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-- 
---------------------------------------
Dr. David Smith
Department of Chemistry
Ludwig Maximilians University
Butenandt-Str. 5-13, D-81377 Munich
Germany
Tel.: +49 (0)89 2180 77740
Fax.: +49 (0)89 2180 77738
e-mail: David.Smith_at_cup.uni-muenchen.de
---------------------------------------

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