AMBER Archive (2005)

Subject: RE: AMBER: Dihedral Energy calculation

From: yen li (chem_me2000_at_yahoo.com)
Date: Fri Mar 04 2005 - 15:29:08 CST

Dear Dr Ross,
Thanks for the needful and prompt help for clarifying
my doubts.

Another doubt(although very basic) is in calculating
the improper torsion.
Could you tell me

i) on what basis AMBER reports the improper torsion in
prepin files
ii) why is it that out of the reported improper
torsions only few are used for calculation of
energies.
iii) do I use the same formula to calculate the
improper torsion energy as that of proper torsion.

regards
Yen

--- Ross Walker <ross_at_rosswalker.co.uk> wrote:
> Dear Yen,
>
> > As Dr. Junmei has stated I am using
> > 0.5 * Vn * (1 + cos(n*phi - gamma))
>
> > Case I
> > hc-c3-c -o 1 0.80 0.0 -1. Junmei et al,
> > 1999
> > hc-c3-c -o 1 0.08 180.0 3. Junmei et al,
> > 1999
>
> > Case II
> > c3-c3-n-c 1 0.5 180.0 -4.
> phi,psi,parm94
> > c3-c3-n-c 1 0.15 180.0 -3.
> phi,psi,parm94
> > c3-c3-n-c 1 0.53 0.0 1.
> phi,psi,parm94
>
> > If I encounter such atom types dihedral, should I
> > i) consider(ALWAYS) all the 2 sets of parameter
> (Case
> > I) and 3 sets (Case II).
>
> Yes you should. So for case one each hc-c3-c-o
> dihedral term would considt
> of the sum of two lots of the equation above. So if
> X is the dihedral angle
> the contribution for each hc-c3-c-o set would be:
>
> 0.5*0.8*(1+cos(-x-0.0))+0.5*0.08*(1+cos(3x-180))
>
> And for case 2 each c3-c3-n-c torsion set would be
> made up of a sum of 3
> dihedral terms with the relevant parameters. Let me
> know if you can manually
> match this up. If you find you are slightly off then
> email me directly and
> we can go through an example.
>
> > ii) since I am doing it manually and there is no
> > problem of over counting 1-4 non-bonded
> interactions.
> > Do the sign of the multiplicity(n) affect my
> > calculation. What does the -ve multiplicity
> signify.
>
> The -ve multiplicity has no effect of the energy
> since cos(x)=cos(-x). So
> since cos is a symmetric function so the -n makes no
> difference - hence the
> reason it is used as a marker for doing the 1-4NB
> calculation.
>
> I hope this makes sense.
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:-
> ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available
> on request |
>
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>
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