AMBER: add waters to a system + leap problem with solvateOct command

From: Fabien Cailliez <>
Date: Thu, 17 Mar 2005 19:30:24 +0100

Dear all,

I have benn running a MD simulation for 6 ns on my system and I would
like to continue
the production. But I have a problem with my water box which is no more
big enough.
Indeed, my molecule undergoes strcutural change, and when I calculate
the minimum distance
between my solute and its image, it decreases in the last ns to fall
under 9 angstrom, which is my
cutoff. I would like to know if this is possible to add waters "around
my current box" (which is a
truncated octahedron by the way) to "push away" the images from my
solute without resolvating
entirely my solute, and thus keeping a continuity with my simulation.
I would like to add a word about the cause of my problem. In fact, I
think I should not have had
such a problem since the structural rearrangement is not very big, but I
remarked that my initial
box is certainly not big enough : altought I asked for a box with edges
lying at least at 10 angstrom
from my solute, Leap does not add enough water. It is the first time it
happened to me. Does anyone
know the reason for such a problem. Is it because of the way Leap
construct its octahedric box, which
might fail for some particular shapes of the system ?

Thank you in advance for your answers,

Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail :
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
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Received on Thu Mar 17 2005 - 18:53:00 PST
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