sander_classic: bellyrun with constraints

From: nicolas baurin <>
Date: Wed 04 Apr 2001 20:13:21 +0200

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,


Nicolas Baurin
Laboratoire de Chimiométrie - Modélisation Moléculaire
Institut de Chimie Organique et Analytique, UMR 6005
Université d'Orléans, BP 6759
45067 ORLEANS Cedex 2, France
Tel: (33+) 2 38 49 45 77
Received on Wed Apr 04 2001 - 11:13:21 PDT
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