AMBER: Atoms restrain

From: Angelo Pugliese <>
Date: Mon, 19 Dec 2005 13:09:35 +0000

Dear Amber Users,

Below there is the input file for a MD equilibration step in which I
want to restrain my 24 residues dsDNA with 5.0 kcal/mol weight and let
the water molecules and the counterions be free to move. Within the DNA
I want to restrain four C1' atoms with a different weight (10.0) in
order to keep the helix overtwisted as I set previously by nucgen.
I wonder if my input file is correct, i mean I am afraid that the
restrain on the whole DNA will overwrite the restrain on the single
atoms and therefore messing up everything.
Thank you for your precious suggestions.
This is the input:

MD on water and counterions
    irest=1, ntx=7,
        ntf=2, ntb=2, scee=1.2, cut=9.0,
        nstlim=5000, dt=0.002,
        temp0=300.0, ntt=1,
Atoms that are going to be restrained in the MD simulation
RES 1 24
Restrain on the C1' atoms
ATOM 9 9 355 355 386 386 740 740

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Received on Mon Dec 19 2005 - 13:53:00 PST
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