AMBER Archive (2004)

Subject: AMBER: constraints on atoms

From: cailliez (Fabien.Cailliez_at_ibpc.fr)
Date: Mon Dec 20 2004 - 05:06:19 CST

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.
 25.0
RES 1 442
END
Atom C from Val 98
 100.0
ATOM 1548
END
Atom O from Val 98
 100.0
ATOM 1549
END
END
*******************************************

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 

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez_at_ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
__________________________________________________________________

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