AMBER: constraints on atoms

From: cailliez <>
Date: Mon, 20 Dec 2004 12:06:19 +0100

Dear all,

I would like to run a constrained simulation on a protein by
constraining 2 atoms
of my molecule to stay at their initial positions.
During my equilibration, I would also like to put restraints on all the
atoms of my solute.
I am not sure about how to write these two constraints in my input file,
because the
2 atoms will appear in two groups.
I suppose that I must write this :
Group input for protein restraints: 25 kcal/mol.
RES 1 442
Atom C from Val 98
ATOM 1548
Atom O from Val 98
ATOM 1549

Can anyone tell me if this is the right thing to do ?
And if so, does it mean that for the atoms 1548 and 1549, the constraint
will be
(100+25) kcal/mol or just 100 kcal/mol, or even 25 kcal/mol ?

Thanks in advance,

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 Mon Dec 20 2004 - 10:53:00 PST
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