# RE: AMBER: Dihedral Energy calculation

From: yen li <chem_me2000.yahoo.com>
Date: Wed, 2 Mar 2005 04:37:01 -0800 (PST)

Dear Dr. Junmei,

"On the other hand, if n is a positive number, the
followed term is for another torsional angle" is not

Stating our problem in detail
H
__ /
H1 N C
\ / \
H2 -- C4 -- C5 -- C C -- H
/ || \ /
H3 O6 C __ C

/ \
H H

In the above molecule
H1 , H2, H3 are type 'hc'.
C4 is of type 'c3'
C5 is 'c'
O6 is 'o' as per gaff parameter.

gaff.dat is reporting two parameters

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

The torsions H1-C4-C5-O6, H2-C4-C5-O6, H3-C4-C5-O6
are
of the same type but Amber is reporting H2-C4-C5-O6
two times and the rest 3 times in the topology file.
I am trying to calculate the same. Therefore I need to
understand how this is done in amber.

thanks and regards,

_______________________________________________________
--- Junmei Wang <jwang.encysive.com> wrote:

> The torsional angle term takes a form of (0.5) * Vn
> * (1 + cos (n*phi -
> gamma)). Here, n takes 1, 2, 3, 4 ...; Vn is the
> force constant for the
> nth Fourier term (the 3rd Field); gamma is the
> phase angle (4th Field);
> n is in the 5th Field of a torsional angle term. If
> n is a negative
> number, the immediately followed term is also
> applied for the same
> torsional angle (more than one Fourier terms for
> this torsional angle).
> On the other hand, if n is a positive number, the
> followed term is for
> another torsional angle. I hope I made it clear.
>
> Best
>
> Junmei
>
>
>
>
> ==================================================
> Dr. Junmei Wang
> Chemistry & Biophysics
> Encysive Pharmaceuticals Inc.
> 7000 Fannin, Houston TX 77030
> Tel: 713-578-6649
> Email: jwang.encysive.com
>
http://amber.scripps.edu/antechamber/antechamber.html
>
> ==================================================
>
> Dear Amber Users,
>
> I am calculating the diheral energy of a small
> molecule for
> which I am using gaff.dat of Amber 8. I have noticed
> that some of the
> dihedral are repeated with different values. for
> example
>
> c3-c2-c2-c3 1 6.65 180.0 -2.
> Junmei et al, 1999
> c3-c2-c2-c3 1 1.90 180.0 1.
> Junmei et al, 1999
> c3-c3-c3-c3 1 0.18 0.0
> -3.
> Junmei et al, 1999
>
> What basis is used for the calculation of such
> dihedral (whether
> all or some are used) and how it is done in Amber.
>
> Thanks
>
>
>
>
>
>

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Received on Wed Mar 02 2005 - 12:53:00 PST
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