Here is the answer to my own request (to make work a belly run (ibelly=1)
with constraints (ntr=1) ),
from dac :
----------------
The constrained atoms come first, then the belly atoms, e.g.:
&cntrl
.....
&end
Title for constrained atoms
5.0
RES 1 17
END
END
Title for belly atoms
RES 32 34
END
END
-----------------------------------------------------
nicolas baurin a écrit :
> Hello to the Amber people,
>
> i'm running a MD for a solvated protein (no pbc) with sander_classic :
> -i want to run a belly around my known active site with a 0.5 kcal
> constraints on these atoms
> -i want all water residues to be free
>
> I managed to do this by use of ntr=1 and declaring water residues with
> constraint constant=0, belly residues with constraint constant=0.5 and
> extern residues with constraint constant=100. It seems that i can't use
> both ntr=1 and ibelly=1 (error message when reading my free residues H20
> [no constraint] ).
>
> So i'd like to know if it's possible to use both parameters (how) and if
> the calculation time is bigger (my way above) compared to a similar run
> with both parameters activated.
>
> Thanks in advance,
>
> Cordialement,
>
> --
> Nicolas Baurin
>
> Doctorant
> Laboratoire de Chimiométrie - Modélisation Moléculaire
> Institut de Chimie Organique et Analytique, UMR 6005
> http://www.univ-orleans.fr/SCIENCES/ICOA/
> Université d'Orléans, BP 6759
> 45067 ORLEANS Cedex 2, France
> Tel: (33+) 2 38 49 45 77
Received on Thu Apr 05 2001 - 00:12:51 PDT
