AMBER Archive (2006)

Subject: Re: AMBER: dihedral angle equation

From: Igor Schapiro (igor.schapiro_at_uni-duisburg-essen.de)
Date: Fri Nov 17 2006 - 08:24:29 CST


Hi Vitor,

you will find the answer on the next page (p.258) in the same manual, if you
read it carefully: "PK is equal to one-half of the barrier magnitude" which
is equal to Vj/2. And the value of IDIVF depends on the substituents of the
bond which rotates. "If all atoms are explicit, then IDIVF=1 ...".

The first equation that you mentioned (p.257) is a general description of the
torsional potential energy function, whereas the second (p.89) is a special
case where IDIVF=1. For this special case the equations are equal.

Best regards,
Igor

Am Freitag, 17. November 2006 13:41 schrieb Vitor Manuel Sousa F?x:
> Dear Amber users
>
> anyone can tell me which is the relationship between in
> the ETirs formula PK/IFDIV (pag . 257 amber 8 manual) and
> the VJ/2 in dihedral equation used by sander (pag 89). The
> two terms are equal ?..
>
> Thanks a lot in advance
> Vitor
>
> *****************************
> Vitor Felix
> Department of Chemistry
> University of Aveiro
> 3810-193 Aveiro
> Portugal
> Tel: 351 234 370 729
 
==============================================================
Igor Schapiro
Universitšt Duisburg-Essen
Theoretische Chemie
email igor.schapiro_at_uni-due.de
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