AMBER Archive (2003)

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

From: sychen (yuann_at_bioinfo.ndhu.edu.tw)
Date: Fri Aug 08 2003 - 10:43:43 CDT

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?

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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