AMBER Archive (2001)

Subject: sander_classic: bellyrun with constraints

From: nicolas baurin (nicolas.baurin_at_univ-orleans.fr)
Date: Wed Apr 04 2001 - 13:13:21 CDT

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