The "excluded atom list" is fairly simple but difficult to manipulate.
An excluded atom "j" is simply one that does not
particpate in a standard van der waals/electrostatic
interaction it atom "i". These are bonded
atom (1-2 interaction), angle atoms (1-3),
dihedraled atoms (1-4) and "improper dihedrals".
There are 2 lists (index i06) which is natoms
long where the value is the number of "excluded atoms"
per each atom. the 2nd list/array (index i08) is
a packed array of the particular excluded atoms
for each atom. (it is acutally an natomXnatom array
with the zeros compressed out).
hope this helps,
jim
On Wed, 27 Sep 2000, Andreas Svrcek-Seiler wrote:
> We are currently trying to modify
> AMBER prmtop files for our own pseudoatom model.
> everything is quite clear except the 'excluded atoms'.
> we would be grateful if someone could tell us
> what this is all about. i.e. what are excluded atoms
> for "atom i" (quoted from the AMBER docomentation) ?
>
> best regards,
> thanks in advance,
> K. Gruenberger, A. Svrcek-Seiler
>
>
> --
>
> )))))
> (((((
> ( O O )
> -------oOOO--(_)--OOOo-----------------------------------------------------
> o Wolfgang Andreas Svrcek-Seiler
> o (godzilla)
> svrci_at_tbi.univie.ac.at
> .oooO Tel.:01-4277-52733
> ( ) Oooo.
> -------\ (----( )--------------------------------------------------------
> \_) ) /
> (_/
>
>
>
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Received on Wed Sep 27 2000 - 09:12:03 PDT
